When you run InnoScript to generate a script and find files in the script that you do not want to deploy, there are two ways of removing them from the generation of the script.
1 - Copy the whole line and paste it into the template file for your project, then add a minus sign to the first position of that line. Of course the line needs to be in the same section in the template file as the file was in the script. This will ONLY remove the file from the one project NOT all future generated scripts.
2 - Add the file name to the unsafe file list. This will eliminate the file from any future generations of ANY project/script. This method will provide a faster scanning for files as the files in the unsafe file list will not be searched for while in method 1 the files will be searched for then removed later after having been found.