Seeing how the problem only reproduces on templates, my guess is that you rely on master pages in your templates. Since master pages are items that are outside the Sitefinity database, they are not handled by our SiteSync module. Some other such items are:
• system data
o non-Database stored content - labels, themes, master pages, etc.
o configuration files (this includes customizations in the backend UI/view and fields definitions)
o configuration about data providers and provider settings
o custom backend pages
o users and roles
o feeds / search indexes
o workflow definitions
o personalization settings
o responsive design settings
Can you please confirm that this is the case and that you have followed the Documentation
when attempting to sync your content?
Ivan D. Dimitrov
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