No, I'm fairly sure the absolute path is kept in the VI. My reference to the project was because I remembered something (probably from Brian Tyler's blog) about the project serving as the appDomain and something else (which may not even be correct, since I'm not a .NET programmer, so it's possible I even made it up) about how the appDomain holds the references to non-GAC assemblies.
That said, I didn't originally read the original question thoroughly, so here are some options:
Make sure they're registered in the GAC instead of being all over the place.
Use a typedef for the .NET reference (you might wish to do that anyway, since I seem remember problems from LV 7.0 where a DLL was upgraded and the reference broke, but that may have been COM). This probably won't help if I understand the problem correctly.
Do a search. I seem to remember someone complaining in the NI forums about LabVIEW asking for similar saves in 8.5 or 8.6.