When you go to delete an Atabeg (garrisoned or not), you end up with -1 maximum Atabegs even if you try to train them from the House of Wisdom.
You get -1 for each delete action, so group deletion of all Atabegs counts as 1 delete action, so it gets -1 maximum Atabeg. If you group delete 3 in feudal, you can build 2 more, but not the third, for example.
This -1 maximum can stack after multiple delete actions, until you cannot build even 1 Atabeg.