CM12 upgrade from SP1 to R2 to CU4

I am in the progress of upgrading SCCM 2012 to R2, we have successfully upgraded half the SP1 secondary sites to R2
Can we upgrade the primary now to CU4 while still having SP1 Secondary sites out there?
Will I be able to upgrade SP1 secondary directly to CU4 or should I complete the full upgrade to R2 across the board prior to CU4, including the client machines?

Upgrading SCCM 2012 SP1 to R2 and have one secondary site server hung. Looking at the Secondary Site Installation Status - it is still sitting at "Register secondary site server controls", and has not progressed since March 27
I cannot see anything within the logs to indicate a possible issue
Is there a way to get this moving and not have to delete the site and dB?
Errors in ConfigMgrSetup.log file show
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_ciid_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_currentcompliancestatus_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_settingid_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.BgbServerChannel.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:08:42 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.DataUpload.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.MessageDownload.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.Usersync.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\AMTEnrollmentServiceWrapper.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:10:13 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching ScanArchivedFiles on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DefaultActionSevere on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DefaultActionHigh on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DeleteQuarantinedFilesPeriod on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Endpoint Protection property matching EventMonitorPolicyBlue on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
ERROR: Failed to create sideloading activations alert for this site. Configuration Manager Setup 3/28/2015 12:11:14 AM 7220 (0x1C34)
ERROR: Failed to create default alerts. Configuration Manager Setup 3/28/2015 12:11:14 AM 7220 (0x1C34)

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<04-25-2014 02:06:46> ******* Start Prerequisite checking. *******
<04-25-2014 02:06:47> ********************************************
<04-25-2014 02:07:00> INFO: Detected current installed build version [7711] for sitecode [BRA]. For Upgrade,
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<04-25-2014 02:07:00> INFPROSCCMCMS.usersad.everis.int;
Unsupported upgrade path;    Error;
Configuration Manager has detected that one or more sites in the hierarchy are installed with a version of Configuration Manager that is not supported for upgrade.
<04-25-2014 02:07:00> INFO: This rule only apply to primary site, skip checking.
<04-25-2014 02:07:00> INFPROSCCMCMS.usersad.everis.int;
Active Replica MP;    Passed
<04-25-2014 02:07:00> INFO: This rule only applies to primary or secondary site in hierarchy, skip checking.
<04-25-2014 02:07:00> INFPROSCCMCMS.usersad.everis.int;
Parent site replication status;    Passed
<04-25-2014 02:07:00> <<<RuleCategory: Database Upgrade Requirements>>>
<04-25-2014 02:07:00> <<<CategoryDesc: Checking the target ConfigMgr database is ready to upgrade...>>>
<04-25-2014 02:07:00> ===== INFO: Prerequisite Type & Server: SQL:INFPROSCCMCDB.usersad.everis.int
=====
<04-25-2014 02:07:00> <<<RuleCategory: Access Permissions>>>
<04-25-2014 02:07:00> <<<CategoryDesc: Checking access permissions...>>>
<04-25-2014 02:07:00> INFPROSCCMCDB.usersad.everis.int;
SQL Server sysadmin rights;    Passed
<04-25-2014 02:07:00> INFPROSCCMCDB.usersad.everis.int;    SQL Server sysadmin rights
for reference site;    Passed
<04-25-2014 02:07:00> INFO: CheckLocalSys is Admin of <INFPROSCCMCDB.usersad.everis.int>.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Site server computer account administrative rights;    Passed
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
SQL Server security mode;    Passed
<04-25-2014 02:07:09> <<<RuleCategory: System Requirements>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking system requirements for ConfigMgr...>>>
<04-25-2014 02:07:09> INFO: OS version:601, ServicePack:1.
<04-25-2014 02:07:09> INFO: Target computer is a Windows server.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Unsupported site server operating system version for Setup;    Passed
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Domain membership;    Passed
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Pending system restart;    Passed
<04-25-2014 02:07:09> <<<RuleCategory: Dependent Components>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking dependent components for ConfigMgr...>>>
<04-25-2014 02:07:09> INFO: Return code:0, Major:10, Minor:50, BuildNum:4000
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
SQL Server version;    Passed
<04-25-2014 02:07:09> INFO: Get Sql edition:Enterprise Edition.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
SQL Server Edition;    Passed
<04-25-2014 02:07:09> INFO: Checking Tcp is enabled to Static port, SQL Server:INFPROSCCMCDB.usersad.everis.int,
Instance:.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
SQL Server Tcp Port;    Passed
<04-25-2014 02:07:09> INFO: Checking if SQL Server memory is limited.
<04-25-2014 02:07:09> INFO: SQL Server memory is limited.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Configuration for SQL Server memory usage;    Passed
<04-25-2014 02:07:09> INFO: Checking if SQL Server memory is configured to reserve minimum memory.
<04-25-2014 02:07:09> INFO: Installing the central administration site or primary site, requires SQL
Server to reserve a minimum of 8 gigabytes (GB) of memory.
<04-25-2014 02:07:09> WARN: SQL Server minimum memory is 8000 MB.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;    SQL Server process memory allocation;
Warning;    Configuration Manager requires SQL Server to reserve a minimum of 8 gigabytes (GB) of memory for the central administration site and primary site and a minimum of 4 gigabytes (GB) for the secondary site. This memory is reserved by
using the Minimum server memory setting under Server Memory Options and is configured by using SQL Server Management Studio. For more information about how to set a fixed amount of memory, see
http://go.microsoft.com/fwlink/p/?LinkId=233759.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Case-insensitive collation on SQL Server;    Passed
<04-25-2014 02:07:09> INFO: Check Machine FQDN: <INFPROSCCMCDB.usersad.everis.int>.
<04-25-2014 02:07:09> INFO: getaddrinfo returned success.
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Validate FQDN of SQL Server Computer;    Passed
<04-25-2014 02:07:09> INFO:CheckSupportedFQDNFormat <INFPROSCCMCDB.usersad.everis.int>
<04-25-2014 02:07:09> INFO: NetBIOS <INFPROSCCMCDB>
<04-25-2014 02:07:09> INFPROSCCMCDB.usersad.everis.int;
Primary FQDN;    Passed
<04-25-2014 02:07:09> <<<RuleCategory: Site Upgrade Requirements>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking if the target ConfigMgr site is ready to upgrade...>>>
<04-25-2014 02:07:09> <<<RuleCategory: Database Upgrade Requirements>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking the target ConfigMgr database is ready to upgrade...>>>
<04-25-2014 02:07:09> ===== INFO: Prerequisite Type & Server: SDK:INFPROSCCMCMS.usersad.everis.int
=====
<04-25-2014 02:07:09> <<<RuleCategory: Access Permissions>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking access permissions...>>>
<04-25-2014 02:07:09> INFO: The rule 'Administrative rights on site system' has been run on server 'INFPROSCCMCMS.usersad.everis.int',
skipped.
<04-25-2014 02:07:09> <<<RuleCategory: System Requirements>>>
<04-25-2014 02:07:09> <<<CategoryDesc: Checking system requirements for ConfigMgr...>>>
<04-25-2014 02:07:09> INFO: The rule 'Unsupported site server operating system version for Setup' has
been run on server 'INFPROSCCMCMS.usersad.everis.int', skipped.
<04-25-2014 02:07:09> INFO: The rule 'Domain membership' has been run on server 'INFPROSCCMCMS.usersad.everis.int',
skipped.
<04-25-2014 02:07:09> INFO: Windows Cluster not found on INFPROSCCMCMS.usersad.everis.int.
<04-25-2014 02:07:10> INFPROSCCMCMS.usersad.everis.int;
Windows Failover Cluster;    Passed
<04-25-2014 02:07:10> INFO: The rule 'Pending system restart' has been run on server 'INFPROSCCMCMS.usersad.everis.int',
skipped.
<04-25-2014 02:07:10> <<<RuleCategory: Dependent Components>>>
<04-25-2014 02:07:10> <<<CategoryDesc: Checking dependent components for ConfigMgr...>>>
<04-25-2014 02:07:10> INFPROSCCMCMS.usersad.everis.int;
Windows Deployment Tools installed;    Passed
<04-25-2014 02:07:10> INFO: CheckAdkWinPeInstalled on INFPROSCCMCMS.usersad.everis.int.
<04-25-2014 02:07:10> INFPROSCCMCMS.usersad.everis.int;    Windows Preinstallation Environment
installed;    Passed
<04-25-2014 02:07:10> INFPROSCCMCMS.usersad.everis.int;
SMS Provider machine has same domain as site server;    Passed
<04-25-2014 02:07:10> <<<RuleCategory: Site Upgrade Requirements>>>
<04-25-2014 02:07:10> <<<CategoryDesc: Checking if the target ConfigMgr site is ready to upgrade...>>>
<04-25-2014 02:07:10> <<<RuleCategory: Database Upgrade Requirements>>>
<04-25-2014 02:07:10> <<<CategoryDesc: Checking the target ConfigMgr database is ready to upgrade...>>>
<04-25-2014 02:07:10> ***************************************************
<04-25-2014 02:07:10> ******* Prerequisite checking is completed. *******
<04-25-2014 02:07:10> ******************************************<04-25-2014 02:07:10> INFO: Updating
Prerequisite checking result into the registry
<04-25-2014 02:07:10> INFO: Connecting to INFPROSCCMCMS.usersad.everis.int registry
<04-25-2014 02:07:10> INFO: Setting registry values
If you wonder whether it might be related to this error:
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I confirm that this one site is a secondary one that's attached to a primary site and this log is from the CAS server, I managed to tall it and delete it from that site, but still appears listed
on the CAS management console, any idea how to force the removal of a secondary site that's attached to a primary from the CAS site when it has been removed already from said primary?
I've already tried the
Preinst /DELSITE XXX command but it only works when the site to remove it's attached to the local site and certainly not from a CAS
Finally, the version, build number and everything is correct, no idea what could be the problem, does anybody know a way to bypass this or force the re-evaluation of this rules, I've got
the impression that it's being cached somehow.
Any help would be highly appreciated,
Thank you.
Marcelo Estrada MCP-MCTS-MCITP-MCSA-MCSE

Hello again everybody,
I've finally managed to fix this up, in the end I had to delete those entries manually from the database as Garry suggested. After this was done the upgrade has gone through as expected with no further ado and has finalized already, now moving on to the
primary sites.
If anybody out there is facing the same issue, what I did was to delete those "stubborn" records executing the following statements over the CAS database:
DELETE
FROMServerDataWHERESiteCode='XXX'
DELETE
FROMSC_SiteDefinitionWHERESiteCode='XXX'
And this is pretty much about it. I'd recommend to take a proper backup first though as best practice.
Thank you all anyways for your answers and comments,
Marcelo Estrada MCP-MCTS-MCITP-MCSA-MCSE

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Information (26278)
VMM could not offload transfer the file \\vm-scvmm2012.domain.com\MSSCVMMLibrary\VHDs\Template_Windows_2008_R2_SP1.vhdx to C:\ClusterStorage\Volume1\VM-NEWVM\Template_Windows_2008_R2_SP1.vhdx.
Any ideas?

I have a similar problem when migrating VMs from Windows 2008 R2 (Non Clustered) Hyper-V to Windows 2012 Hyper Cluster. I had previously migrated about 100 VMs like this with no problem. It appears since upgrading from VMM SP1 Rollup 4 to Rollup 5 this problem
is happening. All Agents are up to date.
I can migrate VMs in the cluster no problem.
I removed the Windows 2008 R2 Hyper-V host and added it back which allowed the job to at least start but when it gets to the final steps of importing the VM it fails with the same error and references the VMM server.
Others suggest this is a VMM Certificate problem and you can remove the Cluster node and add it back again but I can't do that in a production Cluster with hundreds of VMs. That is not an acceptable solution.
How can we fix this?

CM12 upgrade from SP1 to R2 to CU4

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