Quote: If you receive the error, try navigating to the workspace by right clicking on the failed build, then going Advanced->Browse to workspace.
Thanks, that is a good suggestion. I have meanwhile found the cause. If you use a NuGet package that itself is based on Fody (in my case, ModuleInit.Fody), even if all versions are the same, it will not always load the same dependency (not sure why, I have checked settings for each and the settings appear the same). In a single solution of 45 projects I found 8x v2.28.2, 3x v2.28.3 and 14x v2.28.4 (the current version).
The resolution was to uninstall the Fody dependency through NuGet (separate from ModuleInit.Fody, which I left in place) and then reinstalled the latest version of Fody. At each step I needed to check the fsproj and csproj files, because sometimes the uninstall left a build task there.
Once everything was aligned, it worked as it should. Though I am still unsure why there's a difference here, because I would expect that NCrunch uses either version, and since it is only used during build, isolation should *not* result in this error (unless the same process runs the msbuild task on multiple projects in-process, in which case conflicting versions are loaded in the same application domain).