(This is with the current version of the Creation Kit that matches the current version of Skyrim)
I have a mod that I created that adds a cabin to the exterior cell "RiverwoodPath". In order to provide NPC access to the part of the cell where the cabin is I had to modify the navmesh. This worked fine for quite a while. Then one day I noticed that my NPC follower could no longer enter the RiverwoodPath cell via the main road from the south. NPCs would just get to the cell border and get completely confused. I had not made any changes to my navmesh.
I worked on my navmesh for quite some time but could not resolve this issue and could not find anything wrong with the navmesh. Finally I disabled all other mods and found that the problem no longer happend. The NPCs were perfectly happy to cross the cell border. I then re-enabled each mod one by one until the problem started happening again.
It turns out that the problem only happens when I enable a particular 3rd party mod. And that mod is the only one I have that edits the cell directly south of the RiverwoodPath cell. I looked at that mod's navmesh but could not see anything unusual or problematic about it.
Now, finally, my question:
What happens if two mods edit navmesh in adjacent exterior cells? I know that when you finalize an external navmesh it creates links to all adjacent cells so that NPCs can traverse the borders. But, presumably these links would be to the vanilla navmesh in any adjacent cells that your mod didn't modify. Now let's say another mod edits the navmesh in an adjacent cell and finalizes that cell. It would seem that that cell's links would be to the vanilla navmesh in your first mod's cell and not to the edited navmesh in your first mod's cell.
Are my assumptions correct and could that be why NPCs are unable to traverse the cell border when I have both of these mods enabled? And if that is true, is there any way around it? Or is this a case where there is no way to resolve the conflict between the two mods and the user just has to decide which one they want to use?
One other unusual thing is that the cell traversal problem seemed to be somewhat limited to the preferred navmesh triangles over the road. If I led my follower off the road I could sometimes get her to follow me into my modded cell. But, after getting her into my cell she seemed to be following the vanilla navmesh instead of my edited navmesh. I could make my modded cell work perfectly just by disabling the other mod. But, as I said before I don't think there were any actual navmesh problems with the other mod (at least I couldn't see any).