I don't think this has big of a problem as you are making it.

I would just overwrite user created mods, with a warning noting that "Mod X may not work correctly with this version", leave it to the mod creators to change their work. I don't think this is an unrealistic expectation that updates might disable certain mods.

Same for user created content, just make a backup, and overwrite.

I have actual experience in this, just suggestions.

I don't think this has big of a problem as you are making it.

I would just overwrite user created mods, with a warning noting that "Mod X may not work correctly with this version", leave it to the mod creators to change their work. I don't think this is an unrealistic expectation that updates might disable certain mods.

Same for user created content, just make a backup, and overwrite.

I have no actual experience in this, just making suggestions.