These .dat files you see were firstly introduced to resolve the driver letter issue. Drive letters, especially the ones for USB external storage drive, may change. Thus SyncToy need some make to indicate whether a path is the sync folder of current folder pair.
If the .dat file is deleted from the sync folder, SyncToy will not consider it as a sync folder any more. The re-located .dat files affect only if the new location is the same to the original one except the drive letter. Some users tried to copy such files to such folders (which is empty), and SyncToy only copy the new created or updated files/folder to the new location.
It is recommended that such files should not be manipulated manually. If you no longer need a sync folder pair, please delete it by SyncToy. If you need a new backup place, please create a new folder pair. Multiple .dat files can exist in one single folder if it is involved in mulitple sync folder pairs.
This posting is provided "AS IS" with no warranties, and confers no rights.