Rick A. When you rename file outside Tonfotos, it sees it as old file was deleted and new file appeared. If that file contains faces and people names in XMP metadata, Tonfotos will pick it up. However, storing this data into XMP is not on by default so make sure you turned it on. Also, this storing does not happen immediately after you turned it on, so I would suggest you wait for some time (few hours if your library is large) to give time for Tonfotos to push all the metadat into files. Otherwise after renaming you may end up with facial metadata lost. Not that a big deal, since fraces would be typically suggested again, but still not perfect.
Otherwise there are no more best practices. Tonfotos supposed to be tolerant for external editing.
Reindex files will force program to forget the file and read it as it is new one. This is only needed if there was some error when file was indexed first time. Renaming file will make same effect anyway, so no point doing it again, but no harm either.
Rescan folder can be used to make sure Tonfotos scans particular folder for changes NOW. Most typical situation - Tonfotos is busy scanning files in some other place but you want it to pick up the changes that you
just did. By “rescan folder” you force it to look into this folder now and then it will continue what is was doing before.