Sorry, unfortunately it’s hard so suggest anything specific without knowing the exact steps to reproduce it, as there are too many factors that could be causing this.
Our best advice would be to try creating a similar project from scratch (same type, same toolchain, etc), and try comparing the behavior between them. E.g. add the same “hello, world” source file to both test project and the big project and if it behaves differently, try reducing the big project until it matches the small one (e.g. by removing files and settings from it). Once you pinpoint a specific setting that causes the problem, we should be able to suggest a workaround, or provide you with a hotfix.