If a file that has not been synced before by FolderSync exists both locally and remote when syncing and the two corresponding files do not have an identical modified timestamp or checksum (when available for comparison), then you will get a conflict error for the files. The same conflict will happen for a file that has been previously synced, when both the local and remote file has changed since last sync (both files get updated by your or another app with new timestamps and perhaps new content).
To handle cases where you wan't to keep the newest file you can set the conflict option on folderPair to reflect that.
If configuring a folderPair for the first time and you KNOW the files are identical on both sides, you can set "FolderPair -> Sync option -> If both local and remote file are modified" option to "Assume files are identical". This will eliminate the conflicts without resyncing files, and update the store sync data to reflect this. This setting should be temporary.
Potential loss of data
Only use "Assume files are identical" option as a temporary option and only if you are 100% sure the files in both local and remote folder are indeed identical.