OK, since TWC seems really determined to be down, I'm posting this here.
This issue has happened to me twice now, once with Hayastan in Ganzak and once with Pahlava in Hekatompylos. In both instances, the fire temple (Âtaroshan) disappeared as I took the settlements in battle. I'm pretty sure it has nothing to do with the name change (Ganzak doesn't change its name for Hayastan), or the change of ownership (have bought Persepolis and bribed Hekatompylos before with the temple remaining intact).
I'm now pretty sure it has to do with taking the settlement in a field battle, as at least in the second case, it happened after I scored a heroic victory against a relief army plus the defenders. IIRC it was the same case in Ganzak. Not sure about sieges though.
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