Sebastian,
Try removing your local project files, which cause ByDesign to resynchronize your local files with whatever the Server sees)
You can remove them by deleting them from the local folder (though you'll likely want to make a back-up first).
The location of the local folder varies depending on what your studio configuration options are. For example, mine is in Documents -> CopernicusIsolatedShell -> Projects -> (Tenant Name) -> (Solution ID)
Mainly, you're looking for the CopernicusIsolatedShell folder.