Yeah the meshes are there, but the bug makes its as if there was never any nevmesh placed in to begin with. Lydia trying to find a path to you proves this.
This sounds like the software simply isn't loading the navmesh from ESP files if the dungeon is already instanced...Doesn't the game keep the last cell you were in in memory, since there are a lot of times you go back and forth between one zone and several others (like in a town), which would explain why the navmesh is still there if you don't zone twice before returning, so Where I would start looking for the problem is checking to make sure the function that loads and initializes the navmesh is in the code that loads the cell
in the game, and not the code that initially reads the file to get the cell. In other words, it should load the navmesh when you hit the door to go in, not when it reads the ESP file to get the cell in the first place.
it could be storing the Navmesh as a local variable rather than a global one, so when the cell deloads, the navmesh data gets dumped. Given the difficulty I've had making variables retain their values, I wouldn't be surprised if that's really what's going on.
At least if I were looking for this bug, that's where I'd start.