Hi, thanks for sharing this issue.
I think the first thing to try would be to move your V2 codebase to a different location on disk. If there are references from anywhere in the V3 code that touch the V2 code, this would cause them to break (thus highlighting any dependency).
Making any changes to the code inside the workspace that NCrunch has constructed won't help with solving this problem. The code is shadowed and derived from your foreground solution, so trying to force it to behave will at best give you a maintenance heavy solution that will work inconsistently, and more likely just make it harder to find the root problem.
My suspicion is that there is an absolute file reference in here somewhere. It's possible that this is being done at project level (check the ProjectReference tags inside your build XML).
I also recommend having a look at
this troubleshooting page, which describes the rules defining how NCrunch chooses the build platform for your projects. This isn't the same logic as that followed by the IDE, so it's worth checking just to be sure everything is consistent as this is a common area for configuration problems.
