add on sites template update need info and advice

This has to do with a Fiverr Clone theme we are running on a multisite install (not Live yet), We need advice and a little en-site to the workings of themes updating with add on Sites (blogs)

We are using an excellent Fiverr Clone template that has the functionality of everything built into the template and also you can use plugins for extras.
here is my problem and would like hear what everyone thinks. template is called Pricerr and site selling it is SiteMile.

the Pricerr template need to be deactivated and then reactivated in order for database tables / columns to be updated in the install. the way I have it setup is the only template is the pricerr template and its framework (pricerr is the child theme) updates are very often.
I had a problem with a new version not updating the settings until I switched to the framework and then back to the pricerr child template then all was well.
The problem is on the add on Sites not everyone will want to do that and when the template gets reactivated the settings need to be put back in.
How can I
1. keep the settings of everyone's template in place and still have the update.
2. Not have to switch the template on everyone's site to another template or the framework then back to update the database entries and
2a. when that happens does the add on blog have its own database entries for the template?
I just reread this and I guess they have to for each blog to have its own settings.
Andre the developer for the theme is looking into it I figured since you guys / Gals here are experts I can get a fast answers to these questions.
I'm a little confused.