combatReport needs all those txt files, but if you don't use it, you can move or delete them at your pleasure.
tracker reads the pws files, & adds the info from them to its own database file, so you can move or delete those at your pleasure ('cept for the current one!)
but tracker will hork on occaision, in which case you need all the past pws files to rebuild its database from scratch.
wrt the original post, those troops might still be on Canton - a NavSearch plane won't notice them, you'd need to recon the specific hex (sometimes for several turns, esp. w/ low recon skill) to get a radar-return from them. or you could just land-bomb the place, & see if you cause any casualties!