That's what I thought, so I tried it, I'm pretty bummed about losing that interior though. I put a fair amount of work into it. But I have enough screenshots of it that I can recreate it whenever I build up the stamina. I still have the old backups just in case something in the merged file explodes!
But do you think it could be caused by the 0,0 Distance Phenomena?
Nah I had that bug in the middle of Seyda Neen, and have never had this same bug in any far away places I've been working on.
One thing you could try is checking up that puckapfile, but considering you were already opening the thing, I'm afraid it consists the latest changes now.
If you decide to fix the hole thing (if it's more worthy to you keeping the interior) try soften around the empty parts, that usually fixes the land back together for me.