Reloading a Server Project Usage

We've run into a consistent issue where hundreds of recovered elements are showing up in an indirect project usage, being used by elements in a direct project usage. Even if they have been fixed in the direct project usage, they do not go away when updating to the fixed commit of the direct usage. We can fix them by removing, keeping references the direct project usage, then adding it back (with or without changing commits used) and it will resolve the errors.

 

Not something I think can be fixed here but looking at faster options or ways to automate that workaround. Does anyone know the functionality of the "reloadModule" method in the ProjectsManager class of the Open API and whether it behaves in a similar manner to the multi-step process of our workaround for a server project? Any other alternatives we can look at?