Are the files physically still present on the device? Please check using any file explorer. If they are there indeed, then this kind of problem usually happens when either the OS or a third party app is set to clean empty files/folders.
If that’s the case, and the files are present, I’d make sure to set all folders to “Receive Only”, then recreate the folder marker, i.e. create an empty folder called .stfolder inside each of the Syncthing folders. Then try to rescan.