WSYNCMGR.LOG Failed to Sync Update. Failed to Save Update.

Question

I recently had to re-install WSUS on an SCCM 2012 SP1 server which had a problem where the EULA's were not being downloaded by WSUS for any updates which needed them.  Even attempting to download the updates within the WSUS console generated an error
about being unable to locate the EULA file.
I re-installed WSUS with a fresh DB, which caused SCCM 2012 SP1 to immediately expire and remove the updates it had previously synchronised.  This took a horrendous amount of time (at least 6 hours) for it to process all of the changes to the packages
and deployments etc.
This did resolve the issue within WSUS regarding approving EULA'd updates, but I am now unable to perform a software updates sync with the following errors being recorded in the wsyncmgr.log;
Synchronizing update 8e6513d8-dc3a-4468-8108-d44618a6e412 - Windows Malicious Software Removal Tool x64 - January 2008 (KB890830)
Referenced configuration items are not available yet: <MissingReferences><Reference RelationType="1" ModelName="Site_7A5EE138-E14B-4A6F-A5A5-8253002809FB/SUM_2fffa61e-964e-442a-81ad-d822f55d57d8"/><Reference RelationType="1"
ModelName="Site_7A5EE138-E14B-4A6F-A5A5-8253002809FB/SUM_852c74ff-b1b6-4c4a-8490-b0b1d7296d2a"/></MissingReferences>
Failed to sync update 8e6513d8-dc3a-4468-8108-d44618a6e412. Error: Failed to save update 8e6513d8-dc3a-4468-8108-d44618a6e412. CCISource error: 2. Source: Microsoft.SystemsManagementServer.SoftwareUpdatesManagement.UpdatesManager.UpdatesManagerClass.DefineUpdate
These same errors occur for many updates and cause the sync to fail due to consecutive failures.
It looks to me like this MAY be happening only for Expired/Superceded updates and/or updates for which Configuration Manager has previously synchronised.  A handful of updates HAVE made it into the console, but only ones never before synchronised.  I
have searched for and trawled several blog posts for similar errors but these all seem to relate to errors in the objreplmgr.log and child sites - which I do not see any errors in there and this issue is with my primary site.  The primary site DOES however
have two child Secondary sites, so I am wondering if there is a data mismatch somewhere.
I tried replicating the issue in my lab environment and no matter what I did, even hitting some of the tables directly to upset it, I could not replicate the problem to begin to try solutions.
I am very close to having to open up a call with MS, but wondered if anyone had any ideas?
This does raise a few questions regarding DR scenarios too - as to how important IS the SUSDB, how best and when to back it up and if it is expected behavior for SCCM to wipe out it's configuration if it is sync'd with a fresh WSUS install?
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Answer 1

I just can't replicate this in my lab environment, and I am thinking that this is some sort of collateral damage done by the July patch applied by the customer that breaks SQL replication and also causes WSUS Sync issues.  We didn't ever remove that
patch but instead implemented the SQL workarounds but this may just have resolved 'some' of the issues the patch caused.  The annoying thing is that the day we implemented the workaround and proceeded to uninstall/reinstall WSUS and resync SCCM, Microsoft
released the updated version of the patch later that day (UK time) - wonderful timing.
My Personal Blog: http://madluka.wordpress.com