Thanks for the reply Alex. I have Protean and Decorous installed already. When I switched (applied) from one to another on my site, things like removing About from the footer links changed in that it was activated again. I had disabled the About link in Developer but it didn't stay once a different template was applied. Not sure about other things as I don't have a lot of customizations done except for menu changes and permissions but that all stayed the same.

Such changes should be persistent across all templates, the only changes which are applied to particular template are in particular template settings, for example custom styles in Studio > Protean > Styles