If I have active spells on both the cities and I want to change the spell on my primary from one resource to another, I deactivate the spell, but then I can't cast another one. I get the message "You already have an active spell of this school on this city" or similar wording.

Once I deactivate the spell on the secondary city, I can now cast on my primary. And then I re-cast the secondary city's spell to effect the switch of the spell on the primary city.

Currently it doesn't cost me much to re-cast the spell, but it is a bug that could potentially become more annoying.