um... do you mean that the found caches no longer appear in your list of caches or on the map, or that they revert to being marked as unfound? If it's the first, then your filters are simply set to hide your finds and they are actually disappearing while your device is on. If it's the latter, that is unusual behavior that should not be happening. The device reads your field notes (both the .txt file and the .xml file) in addition to the status written into the GPX file to mark caches as found. This is also how the device can distinguish between a DNF and an unattempted cache. Either you didn't mark it as found, or went back and marked it as unattempted after you found it.
The latter can happen if you delete the geocache_visits.txt and geocache_finds.xml files, but not update your pocket queries or cache files.
The geocache_visits.txt file is what you need to upload field notes (located in /GARMIN/Garmin/). It's a good idea to periodically delete this file (and the xml file) *after* you import your field notes as this makes sure the GPS is properly indexing a fresh file each time you run your PQs.
So, should I delete the geocache_visits and geocache_finds files and create them back?
BTW, I noticed that these files, geocache_visits and geocache_finds are indexed in the Filters folder. Im pretty sure I never touched these files before.