Hey Remco,
I went ahead and tried reproducing it on a simple 2 library project and was unable to do so. Basically the majority of my debug session was moving files between projects, updating namespaces and changing references between projects to fix errors as I changed what was in which namespace. I guess this will just have to be one of those issues I'll keep an eye out for and if it happens again maybe I'll figure out some new details.
Thanks,