Upgrade subsets with latest features available

Hi,

I'm working in a multisite wordpress SAAS application. The main site is the marketing site for the product and people can auto register for its private subsite.

I use blog templates so people could get a copy of the system as they register and have the required functionality.

In their own subsite, people has is own private zones where they manage documents. There's no post or pages and no public site, all is viewed by users with an account on their site.

My doubt and pain right now is how to manage upgrades a new functionality for people registering.

Right now I upgrade the "template blog" that I use for people registering in the site, but as they get a site, they are stuck in that template blog version. If I upgrade the template blog with new Custom post site or a update of a CPT already in place, existing users can't get that changes. Only people registering.

This is a huge problem for me since if there's no solution for this, it would make the system not viable in the long term.

Someone could share the methodology or the way to deal with this problem?

Thanks in advance.