Really, at this point we work with assemblies that was translated.
Looks like ProcessSkippedAssembly now is not good name for function - maybe better name will be PostProcessAssembly or something like this. 
Before my commit you've called it once for each skipped assembly and once for "main assembly" (assembly to translation from command line parameter). Bad thing is that I've not found good way for list of all translated assemblies with their path, so I try to guess this pass from translation result. If there will be better api, this code will look better.