I know this bug existed in 8.1.2 or earlier and it persists in the current version of 8.3.7. If you open the Poke Editor for a Pokemon who had some PP Ups or PP Maxes used on some of its moves, those increases are removed.
How to reproduce:
1) Use PP Ups or PP Maxes on one of your Pokemon
2) Put the Poke Editor in your hand and use it
3) Click the "Edit" button for the Pokemon you used the PP Ups or PP Maxes on.
4) Click "OK" (you don't need to make any changes).
5) Go into the Pokemon's Summary and check its moves. The PP Ups and PP Max boosts are gone.
Tested using the The Pixelmon Modpack on CurseForge.