UE5 name.project requires a temporary target.cs to be generated (Water plugin is enabled)

I have thought the same.

A good test would be to try installing UE on a clean machine and move a copy of your project there.

If the issue still persists I feel like it is fair to assume that it is definitely UE / something within the project that has gone wrong.
Could also try to create a new project using the same plugins etc. but on a different machine.

Just brainstorming a bit, unfortunately it put me off using UE for a bit and will have to return to it later. Had hoped I could go to UE4 instead of UE5 to fix it, but it sounds like that isn’t a viable plan.