• On the DFSR server open Command Prompt as Administrator
• Run WMIC.EXE /namespace:\\root\microsoftdfs path dfsrreplicatedfolderconfig get replicatedfolderguid,replicatedfoldername
  Copy GUID of the folder you want to clean
• Run WMIC.EXE /namespace:\\root\microsoftdfs path dfsrreplicatedfolderinfo where “replicatedfolderguid='<Folder GUID>’” call cleanupconflictdirectory
  Replacing <Folder GUID> with the ID you copied in the previous step

Windows Server 2008 R2
Windows Server 2012