API restriction generating same file twice


I have a .NET project which contains identical files, but the files originate from different directories. While writing the satellite assemblies for this project the duplicate files are not written because of an "API restriction - The assembly "{0}" has already loaded" (Messages). Why does Passolo not support that? My current workaround is to restart Passolo and generate the remaining files. Some files are three times in the project, so I have to restart Passolo everytime, to write the remaining files, that could not be written because of the API restriction. So I am not able to automate Passolo by batch and have to do it manually, which is not convenient.

Is there another workaround I can use?

Thank you in advance.

Best regards