This needs to get fixed sooner than later. I switched distros yesterday and when I logged in all my settings got reset to the defaults it seems, so the Steam Play for all games thing got unchecked and I was forced to start downloading all my damn Windows games yet again. Nothing but a manual uninstall should ever remove games from my system ever! There is no reason for this nonsense.

this happened to me after proton 3.16-8 beta was released, so looks like i'll be spending the next week redownloading a shit ton of games lol

This happens without even disabling steamplay or changing any settings. Sometimes the updates are 400MB, sometimes it has to download the whole game again.

I can confirm that it is still an issue.

Also a way to see the Steam whitelist within Steam even with proton enabled for all games would be welcome(related as that's why I disabled proton for all games).

After updating to a custom version of Proton, for some reason the "Enable Steam Play for all other titles" checkbox got unchecked by itself and Steam decided to erase a 50GB game.

Would be really nice to see this fixed. Sometimes you just want to toggle between Proton versions without redownloading the whole game.

I can confirm that this is still an open issue. I just toggled off and on the "Enable Steam Play for all other titles". The app restarted each time. Once re-enabled I had to re-download hundreds of gigabytes. This seems unnecessary and less than ideal.

Why... on earth... is this an actual thing?

I must concur with Uradamus' comment above.

Unchecking the box instantly removes the game? There absolutely must be confirmation dialogs on data deletion.

I just lost my game install and am now required to download another 55GB of game files.

Edit:
For further clarity:
Unchecking "Force the use of a specific Steam Play compatibility tool" did NOT uninstall my Halo Infinite installation.
But it DID uninstall my Batman Arkham Knight installation.

Why... on earth... is this an actual thing?

Yes. Just happened to me.

Unchecking the box instantly removes the game?

Not instantly. However for a certain amount of games it prompts an "Update" of whatever the game's size was.
When Steam inevitably automatically starts that update, it deletes the game's files.
IF you were lucky and it didn't start the update, you just have to verify integrity of the game and it's back to normal.
Hope this helps anyone, so if you were switching Proton versions or anything that might cause this issue, maybe disabling automatic updates beforehand will save your day.

I hope this get fixed soon, thanks Kisak.