I deleted the vanilla navmesh in the interior cell, the Four Shields Tavern in Dragonbridge. I set up my new navmesh and finalized it and no problem. Went in game to check it out and saw that NPCs were trying to exit through a door that have been moved now to the other side of the room. Then the game crashed.
I went back into CK and after loading saw that the original navmesh had reappeared along with my new one and now I have a double nav mesh. So I deleted it all and started again.....went ingame to check and the same problem with NPCs. Reloaded the CK and it is the same thing, a double navmesh with CK warnings about refinalizing the navmesh.
I have no idea what to do at this point.....if anyone has any ideas I would be very grateful.
your problem here is obviously you didn't finalize your new navmesh.
if there's a door, there's an according door-triangle on the navmesh (green after finalizing), which is assigned to the navmesh when you finalize.
npc's will assume this triangle as the door, not the actual door-item, so without finalizing, if they try to get out, the only door-info they'll find is on the old, deleted navmesh.
that's why your game crashes, because they try to move onto a navmesh that's no longer there, and that's why the old nm doesn't get deleted, because the door-reference from whatever is on that door's 'other side' still points to the door-triangle on this nm.
apart from that, i strongly second everything arthmoor said about not deleting navmeshes

(though for interior nm's with no doors or any other nm's bordering it, it might be more or less safe, but that's certainly quite some ifs to many for any kind of recommendation
