Hello everyone. I also have had a mysterious glitch where my holy city (which is also my capital) loses the holy city status for no apparent reason. This happens only in some games. I don't usually notice until Theology/the HC wonders, but I noticed it more recently this last time.
In this game, I have not reached Theology yet (still in the Classical Age), no other religions have been founded by Civs I have met, so no trade routes, inquisitors, etc. It frequently happens when I play Germany (my favourite civ), but it's happened at least once while I was the Shoshone. The mods I use are fairly minor, but also happen without these mods/in vanilla BNW. I have never used the IGE mod.
I actually registered on here just because I found this thread and wanted to add to it. I hope an answer can be found, as I so thoroughly enjoy Civ V and using religion to help take over the world is a part of my strategy
UPDATE: I went back to my game, via autosaves, and checked my holy city every turn. It lost its status on the transition from turn 328 to 329, for no apparent reason; my religion is the only one I have contact with, so no GPr or inquisitors or my own doing that way. Quite simply, one turn it says Holy City, the next it doesn't. These are screenshots of the before and after. First, turn 328 where Berlin is the Holy City of Apophis:
http://cloud-2.steampowered.com/ugc...09BA3D83B4A43A1B9AB7F6F/1024x639.resizedimage
Now, turn 329, where Berlin is merely a city with Apophis:
http://cloud-2.steampowered.com/ugc...2764083E27AE90BDAF4A74E/1024x639.resizedimage
This happens regardless of using the System Lords mod (changes religions to Stargate System Lord religions) and I have played as Germany with Apophis before without this happening.