We have test cases to check that such a use case is behaving correctly, and we do not have such issues.
Please can you provide an archive file containing your IDE V1 projects (without source file or only fake ones if you want, and without build output (ads/rvds/gcc directories) to make the archive lighter)?
It will let us investigate the issue.
By the way, please can you also provide the backtrace associated to this NullPointerException (contained in the .log file of your workspace)?