I just discovered that LGNPC Vivec Redoran, in the process of editing the Redoran canton, renamed the Underworks. (I assume this was accidental.) Instead of "Vivec, Redoran Underworks" it became "Vivec, Redoran Underworks" (extra space after the comma). This doesn't matter by itself, but if you combine it with another mod which changes the Underworks, the other mod's changes don't show up because the game thinks they're in a completely different cell. In my case I was playing through the Suran Underworld mod, and couldn't find a door which that mod had added to the Redoran Underworks.

Edit: it seems that the extra space after the comma doesn't show up in the post. I did type it, though.

It kind of looks intentional to me. Inside the plugin you can see that the doors that go to the Redoran Underworks are replaced with doors that send you to the renamed cell, apparently for the King Rat quest.

John is correct - the cell name was a conscious design choice. To control the potential for conflicts with other mods that alter the Redoran Underworks we created a new cell. This was not for the sake of King Rat but for Soul Sickness in an Orc. The latter quest alters existing elements in the Underworks. The new cell name is subtly different to make the change as seamless as possible. The teleport doors to the Underworks are not altered, but new doors overlay the original and are enabled when the quests becomes active. This approach makes it possible for the player to disable the teleport doors to the new cell through the console to access the original Underworks should it become necessary. This is explained in the readme. If a player would like to preserve access to both versions of the Underworks, do not disable all of the new teleport doors.

OK, thanks. I guess I should have read the LGNPC readme before I posted. I probably did read it when I loaded the mod, but didn't realize at the time that Suran Underground changed Redoran Underworks, so didn't think I needed to care about disabling the doors and forgot about it.