If a .csproj contains a <ProjectReference> which is not in solution, even though VS2012 has no problems building it, the UI still has troubles resolving the reference. I.e. Solution Explorer displays reference icon with with that little warning overlay (I've attached a screenshot). Since VS has no issues building the project, the only problem was Resharper not resolving this reference either. This issue existed in VS 2010 (it's a known VS bug), but at least there was workaround: close all opened source code documents, close VS, cross your fingers, load solution again. And, if you're lucky and don't have too many VS plugins, the references would load resolved. In VS 2012 such workaround no longer worked, thus we were forced to include all referenced projects into a solution file, or add references as dlls, not as projects.
What I'm seeing right now is even though VS2012 still fails to resolve references and still displays those warning overlays, few latest Resharper EAP builds have no problems picking up assemblies from what appears to be target path of referenced project.
I don't know what changed. But I hope this was an intentional change in Resharper :), and if so, thank you a lot!!! And keep up the good work!!!