Some Context is lost after Project Rebuild

Hi!

I have a maven project (using version 3.3.9) with Spring with several modules which runs fine on both Tomcat and Websphere. But each time I rebuild (Ctrl + F9) the project, the search for method usages or implementations of a method return not all usages/implementation or none usages at all.

I can fix this problem by either invalidating caches or editing the Project Structure, so that the "Apply" button becomes activated. After selecting "Apply" the usage search works fine until I have to rebuild again. 

What can I do so that I don't need that workarounds?