Yeah, I was afraid that was the case. It's along the same silliness line as requiring a manual update after changing an entity, having to deactivate to modify (why oh why) or having to select the verification certificate when I already told it what SP to use (which their metadata contains all that info...).
Managing hundreds of partnerships is very difficult with the current state due to such a huge disjoint between partnership -> entity -> context template -> cert store. Would be nice to have a simple happy union of all of them.
As it is there's so much clicking, having to create copy active/re-activate to avoid an outage, get updates, apply update, confirm, submit, test, and move onto the next. It almost makes using the context templates useless, cause once you use it across a bunch of apps you better never change it or plan for 2 weeks of coordinating updates with the app owners .
Will look into any ways to do this...cause manually updating a ton of them would be very very painful.