Is this an issue? My dungeon design guy had to change some stuff outside a cell, and he took pains NOT to delete any navmesh, instead moving them around.

http://i1295.photobucket.com/albums/b630/Matthiaswagg/Screenshot174_zps02103e25.png

In a custom worldspace, you can delete the navmesh and remake it once everything is in place. It's only in the vanilla game that deleting them can cause problems. Otherwise, I'm not enough versed in navmeshing to understand the message. Sorry.