A DynamicNavMesh within a NavMeshBoundsVolume placed in a SubLevel will disappear if loading/unloading another SubLevel that has completely nothing to do with the DynamicNavMesh. Using a setup with LoadLevelInstance or LoadStreamingLevel produces the same outcome.
This was reported and tested in 4.20.3 (CL-4369336). This was reproduced in 4.21 (CL-4541578) and Main 4.22 (CL-4553454)
Results: When Sublevel 2 is loaded it will unload the navmesh from Sublevel 1
Expected: Both Sublevels can have their navmesh loaded at the same time.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-66340 in the post.