Branch switching: closed projects

I'm a new user with EGit (after years working with Subclipse).
What I like very much with git, is the easy and fast way to switch from one branch to another. This is also a feature of EGit. But, there I have some problems.
We have an Eclipse workspace with about 80 subprojects belonging to our application. Recently, we changed subproject names in development branch for some reason. So, now I have the uncool experience that after changing the branch my Eclipse workspace comes with compile errors. Obviously this is due to the fact, that projects, which the former working branch did not know, are presented as closed projects after branch switching . And, vice versa, projects, which are not existing in the branch where I switched to, are still visible in the Eclipse workspace, although as closed projects. On disk I can see, they do not contain source folders, they only the "bin" have subfolders with compiled classes.
This is not consistent to using git on command line. If I do a checkout on a branch, the work area is truely clean, no project folders are existing which do not belong to the current checked out branch.
Maybe I'm doing something wrong? Any tips welcome.

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