Ugh, ugly.
Is there something I did wrong?
No. Structs behave so much better than they used to but there are still issues. What you describe may happen when you reference an exposed struct and then modify what’s included in the struct. Struct nesting can also be a pain the neck 
There is one thing you can try but it’s not guaranteed to work.
- shut the editor and make a copy of the project
- open the project copy
- fix the struct (as you do) - refresh, compile, save all
- open the struct and make some changes, add a variable
- save the struct
- do not save anything else, do not compile
- quit the project, do not save, reject all prompts, cancel and whatnot
- open again and see if it works better
If it does, apply it your original project (after making a copy).