在基于Linux的发行版上签署Windows应用程序

I have prepared an application and website where the customer can set several options for this application before he downloads it. Settings are stored in binary format on the end of the file (appended), then the edited file is sent to the end user. The problem is that the change of "contents" of the file will break the file signature - is there any chance to re-sign this changed file with any command line tools? I've tried to use Microsoft's SignTool, but it does not work properly on Linux.I have prepared an application and website wher