Merging project/solution files is a well-known disaster among developers/SCM admins performing merges in their source control.
Take, for example, a common scenario:
I've written a small Perl-script to merge solution files: http://blog.tedd.no/index.php/2011/01/06/merging-multiple-visual-studio-solution-sln-files-into-one/
The script could be modified to suit your needs.