So.....is the best way to deal with an interior vanilla nav mesh, to move the entire vanilla nav mesh out of the way and then create an entirely new navmesh?

So you end up with an untouched nav vanilla nav mesh and your own nav mesh. This would circumvent the 'deleted' nav mesh problem? Would it create problems with other mods that modify the vanilla nav mesh in that cell, or create their own nav mesh?

GIve the vanilla NavMesh an EditorID before you otherwise edit it, then amend it and it'll not be deleted. The "deleted" NAVMs seen in DLC are accidental as the CK will delete and replace the NAVM when the user only intends to modify it. Adding an EditorID circumvents the unintentional switcharoo. Particularly if said NavMesh is connected to any doors, you'll not want to replace it.