Just to add someting to DUMMY mechanics and how it works under normal circumsatnces.
Let's say you create a player. I DO NOT KNOW what ID the game assigns to him. You start a Master League he is inside fair and square.
Going back to edit mode and defaulting him , (NOTE: If you registered him in a team, you cannot delete him, you must first release him as free agent, and then delete him from created player slot, IN A CLUB you can only default him) he returns back to generic appearence , with right foot, and OPR of 85 IIRC, all stats are the same for him.
Going back to ML after this, he is still in your team. His stats, special skills (except for COM) and AGE, nationality, cannot change, it stays as they were when you started the ML.
But whatever can be changed, aka appearence, prefered foot, movement, name, is changed, with the usual generic face.
Maybe when a database-datapack update happens, a similar situation occurs that removes the players from the database by force. I do not know why, maybe some IDs do collide with KONAMIs used/new IDs...
As for the memory capacity, as far as i recall, the EDIT00000.bin is almost the same file since PES 2008. So basically KONAMI uses this structure since 2007, the early PS3/XBOX360 days. So indeed it is an old and aged database structure, that why there are so many limitations.
After the 2019 fiasco, 2nds divisions and unplayable THAI league, they were supposed to upgrade those old files, in order to fit all those "new teams", but i assume what they technically did upgrade, was just a cheap expansion to the current database system.
They did not updgraded to something newer/bigger/better/more modern they just tunned it to have a little bit more space.
I think the team behing smokepatch and other PC modders have deeply explained it, how it works in collaboration with the .exe, PS4/PS5.app and bits/bytes, hex editing. In the EDIT00000.bin file they can create some thousands of additional teams/players, but in the game it can be displayed as playable/visible almost only the teams and players that appear in vanilla/factory game, with some minor additions.
If they really jump to new engine next year, Unreal Engine, they must also upgrade the rest assets, database, system settings, to something more modern. It will need modding work to be done from scratch, and scrap all last years projects, but i hope it will open new paths, for more leagues/divisions/players/kit slots/image slots.