Now just finishing parsing the references again, took a bit longer than 40 minutes.
I found also reason to this issue. It seems this issue is escalated already to MS Connect and discussed in Silverlight forum.
The project references are some reason lost when using the direct project reference. If you use the file based reference then the error message disappears and I you reopen
the solution without doing this exercise again.
Are any of you experiencing this reference issue when trying to recompile the ChangeSet(s) or is something wrong in my environment?