By Default the difftool has

scanMode=diff_only

This is just for logging and doesn’t fix items

The fix items : 

scanMode=comparison_now
hasWorkspaceContent=true (if you have Workspace CE)
hasMetadataContent=true (if you have Metadata CE)

Please ensure you run it after hours (after synctool has run) or increase the synctool schedule. Difftool will pick all those documents in Active Content and will reindex them, so to avoid duplicates you should be running the diffscan once the synctool has finished processing.