There is a great post on Technet on Manually Clearing the ConflictAndDeleted Folder in DFSR, however it was written back in 2008 and it seems things changed slightly, so I thought I better write a quick blog post in case anyone runs in to the same issues I did.
Please refer to the above article first, I had issues running the CleanupConflictDirectory method.
WMIC.EXE /namespace:\\root\microsoftdfs path dfsrreplicatedfolderinfo where “replicatedfolderguid=’70bebd41-d5ae-4524-b7df-4eadb89e511e’” call cleanupconflictdirectory
Description = Invalid query
Switch the quotation marks around so instead try:
WMIC.EXE /namespace:\\root\microsoftdfs path dfsrreplicatedfolderinfo where ‘replicatedfolderguid=”insert-GUID-here“‘ call cleanupconflictdirectory
This should work! (If not, are you using an elevated Command Prompt?)
For more information on how to clear the ConflictAndDeleted folder please refer to the blog post here: https://blogs.technet.microsoft.com/askds/2008/10/06/manually-clearing-the-conflictanddeleted-folder-in-dfsr