When it comes to .Net, Fortify can only scan assemblies that have a .pdb because it uses ildasm.exe
to decompile the assembly and then it uses the .pdb to match to the source files. Unfortunately there is no way for you to scan these extra assemblies.
If you have the .pdb files, you can have Fortify scan them, however you may not see the full source in your results. To include these assemblies, you need to specify them in your Translation options. If you are doing this all from the command line, then this is how you would do it:
sourceanalyzer -b project -vsversion 10.0 projectPath\Additional.Assembly.1.dll projectPath\Additional.Assembly.2.dll projectPath\Additional.Assembly.3.dll
sourceanalyzer -b project -scan -f MyResults.fpr
If you have not yet updated your Fortify version, I would highly recommend that you do so.