Hey, Had the same issue.
I found if you remove the RecastNavMesh as well as the NavMesh before adding a new Navmesh it seams to fix the problem. The Recast is added when you drop a NavMesh into the level but not if one is already there.
At a guess i would say its not re-targeting to the newer NavMesh and i cant see a way to change or set the target.
Hope this helps