Yup, need to backup each module. Some take pictures or write down the original settings before making changes.
If I am understanding your predicament, you may have to use the option that says "Download As-Built" or "Download AB" or something like that in each module that got borked. Update your VIN in each module to your real VIN before you download so that the correct as-builts are downloaded for each module.
Worst case, Jesse will be able to walk you through everything.