I once disabled it and indeed I lost all of my progress.

that's not nice at all
Sometimes i just want to play the vanilla isaac

what clears the save is usually when the mod gets updated. subscribe to mod compatibility hack, it will back up your saves.

nicalis has given us a god awful api that cant even handle saves right. i assure you that progress being cleared is not what we want.

so in theory, the saves will remain if i disable and have mod compatibility hack?

as long as the mod compatibility hack mod folder doesn't get deleted, your progress will be fine.

ok thats great, because my computer is bad and even with the settings of particles and stuffs off, the fps drops to 40 when revelations is on, so i dont want to play the normal path with the revelations on, or my frames will be bad