I have tested the pro sites module "Premium Plugins" on my site with 3 pro sites levels:
- basic - default plugins some network other site activated
- premium - here I've set 2 plugins with auto activate option
- complete - 1 plugin with auto activate
After upgrading to higher lever the plugins are not activated. I tested with manual upgrade and with Stripe (test mode).
Could you please check that out, I granted the access to my website.