DFSR Question about the DFSRPrivate folder

Hello all and thanks in advance for any info you may provide.
I am using DFSR for first time and I face an issue with the replicated data and the source data. I want to clarify that I am using DFSR only to migrate data to a new file server and after the replication is completed I will decommission the olf File
Server.
My problem is that when I go to check the source and the destination data, they don't have the same size (which is expected, as I thought that some files, if they are opened or in use, they cannot be replicated). Well, it seems that this is not true,
because I checked it in a test environment. So, after I tested it and I saw that everything is replicated, even the opened files, I was wondering why the source and the destination data are not the same. I believe that there's not any problem if
I miss 500-600 files, because these files may be temp files, or bak files. When I run the report, I see that the files that are not replicated are basicaly pdf,docx,xlsx files. So, why these files are not replicated?
A colleague explained me that the difference between the source and destination data occurs because I have left the DFSRPrivate folder which contains the staging folder in its original location in the replicated folder. He advices me to change this, which
is a huge workload for me now. My question is, does my colleague have right? Shall I change it? If you leave the staging folder to its original place, will this cause any trouble?
Thank you all!

I would not move the staging folder.  I have NEVER seen a Microsoft document that recommends that, for any reason.
Have you checked the DFS Replication logs in Event Viewer (under applications and services logs)?  Do you see a lot of 4304s?  That may be the reason that the pdf, docx and xlsx files aren't getting replicated, they may be in use. (the same file
on more than one server)
How is replication progressing?  Is there a backlog?  There is some information in this article on using the backlog command:  http://blogs.technet.com/b/askds/archive/2007/10/05/top-10-common-causes-of-slow-replication-with-dfsr.aspx
Also, to check what state the replication process is in, use this command:
wmic /namespace:\\root\microsoftdfs path DfsrReplicatedFolderInfo get replicatedFolderName, State
0: Uninitialized
1: Initialized
2: Initial Sync
3: Auto Recovery
4: Normal
5: In Error

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