Commercial building upgrades are, in my opinion, flawed as of right now.
To upgrade commercial buildings, they need only two things, happiness coverage (services/parks etc) and high wealth shoppers, as soon as those two things happen the stores will upgrade instantly and at level 2 will demand more educated workers to operate them. At this point if you don't have enough educated workers for the store it will be abandoned, afterwards, whether you demolish it or just wait for it to rebuild itself, as soon as that new store gets a single worker, it will upgrade again instantly to level 2 and demand educated workers. This is a repeatable loop scenario that can only be fixed by removing happiness coverage to limit the upgrade, or to wait it out until you have the educated workers for the store to operate.
The same might be the case with industrial as well, but I rarely have happiness coverage on those zones.
There is a fix that CO can make to this behaviour, and that fix is to simply disallow commercial (and industrial) building upgrades until that building already has enough educated workers for the upgrade to be successful and for the building to keep operating. Secondary to this initial fix they could add in some selective hiring, so for example;
1. Building is ready to upgrade - Check employee education level, if too low, move to 2, if good enough, move to 3.
2. Upgrade disallowed, start selective hiring process - To upgrade building we need X educated workers, prioritise these positions as uneducated workers leave/die. Return to 1.
3. Building is ready to upgrade, staff education level is adequate for building to function if upgrade occurs - Upgrade building.
In this fashion it would fix the repeating loop in that all building abandonment due to uneducated staff would stop, this would still allow for abandonment due to not enough staff in general.
For anyone who is about to reply with "This will take more processor time etc" please consider that at current the processor is wasting cycles with the repeating loop for every single building this happens with, if anything, this should reduce overhead and limit the need for players to have to keep happiness services away from upgradable buildings until they have sufficient education levels.