Repeating Yossar's question: Check the province(s) your Arch Theurgs were in before Gateway-ing. If the troops aren't there either then you have a real problem.
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It's just a dogma-eat-dogma world...
no, it seems clear that the armies dissappeared. i would think this is definitely a bug. Gladiators i could see dissappearing, since that's what they're best at , but not principe.