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So I've been playing through the game again and when I was travelling to Nighon I ended up at a different exit when I left Thunderfist. It seems like all the entrances were shuffled. I'm playing with the newest grayface patch installed. I went and checked it without the patch and the entrances are placed how they normally should be.

Has anyone else had these changes in their game?
Yes, that is an intended change in the GrayFace patch (made either in 2.2 or 2.1). The point was that the eastern exits should make you leave at the eastern entrances to the caves and vice-versa, or something along those lines. I'd have to double check how it is with the patch, but it's meant to make more "sense".

Edit: Indeed, there are 4 exits to Nighon: NW, central, NE and E. Each one leads to the respective part of the map with the patch.
Post edited May 27, 2019 by Jann180