[1618] Code analysis doesn't fix itself after updating reference

I have a project that uses an external dependency (StructureMap), I started my upgrade process of removing the old version and replace it with a new version.

In my solution I have a folder called Library that stores all external dependencies, inside this is a sub folder for each dependency along with a folder named for it's version so

Proj\Library\StructureMap\v1\

When I upgrade references I will physically delete the v1 folder then create a new v2 folder with the new assemblies. Clean and rebuild my project which should then cause 100% build failures for the dependent projects. I do this to make sure VS2008 has removed every location of the previous DLL (I've had way too many nightmare occurences of dealing with lost old versions of assemblies)

Resharper then correctly realizes my entire solution now has code errors. However when I edit the individual project files to delete the reference then add the new reference the projects will build successfully yet they will still be marked in red as if the errors were still there also the solution wide analysis will not update any improvement.

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