My eyes aren’t that great, so I hadn’t seen any overlap in the images, but yes - that will break the navigation.
Nav volumes are searching for a “floor” on which to walk, if you have one floor over within the same volume it will break.
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If you can make the volume “short” enough not to involve the higher floor it should fix the problem.
Testing to see if a location can be reached from another is pretty simple.
Make a blank Character class, and put something in it so you can see it (a sphere parented to the “Mesh” or similar.)
Attach a pin to BeginPlay → [Ai MoveTo] (the target location).
And click on the inherited Movement and adjust the Max Walk Speed down to 50.
Drop the dummy actor at the starting point and simulate.
If the path is valid it will move to the target.
Otherwise you will need to correct something (almost always the Nav Volume)