My suggestion to fix this problem? Tell modders to stop updating 5 times a day and think about their user base. If you need to update your mod that often unless it is a emergency fix it isn’t ready for the public. This needs to be drilled into modders heads. Also you can hide or make private mods that you are just testing. Or make a duplicate for testing and only upload ones you know work. I’ve been ranting about it forever. If you want people to use your mod make it user friendly. Even better - give a warning you are doing a update soon or better then that have a set update time. Sorry I know this doesn’t help with your immediate problems OP but yeah, tell the mod authors this is a real problem that they have control over.
Maybe I’m misunderstanding you but couldn’t you just copy your game.ini before a reboot? Or is it automatic?