I just fixed a similar issue with a VS2010 solution with 42 projects… The cause was a duplicated
section in the solution file. I closed the solution, removed the duplicate GlobalSection(TeamFoundationVersionControl) config and reloaded the solution and the warning message was gone.
Hope this help!
“Unable to write to output file [FileName] .pdb: Unspecified error” for one of the projects.
I have cleaned the project solution , deleting references but that didn’t help
Figured out that there was a missing file in one of the projects. To know which file it is please follow the steps
 Close visual studio
 Reopen the solution (DON’T build)
 Check the Errors List
You should see
Error 1 Unable to open module file [FileName].vb : The system cannot find the file specified. [FileName] [Project]
Hope its helps!