I see the problem. Sync Template is basically syncing each template set against each other. While this working great with the original template set, the custom ones have different site_header and site_footer templates.

I have some good and bad news here:
The good news is that all modified templates can be restored with the undo function. The bad news is that I just discovered a bug that the sync script that will escape the undo templates twice

To fix the problem, open both site_header and site_footer of all template sets in the template editor and select the undo option below.

Now copy the HTML part of each restored template set to your favorite editor and doing a search and replace for \" to " and \' to ' . Then copy it back and save it.