Trust hotfix for how writes land.
Every edit now changes exactly what you asked for. PKHeX's slot writer was quietly marking the Pokédex seen and caught, bumping trainer records and rewriting handler data on every write, so even sorting a box touched data you never edited. Slot writes are now surgical: the dex, records and handler data only change through their own editors.
Gen 3 and 4 get honest PID handling. Nature edits keep shiny Pokémon shiny, gender and ability edits land on Gen 3 instead of silently reverting, and Gen 4/5 gender edits stay consistent with the PID so mons do not come back flagged. The batch editor got the same fix.
New About screen with the version and credits. Logo by @SpritedMistery.