is it possible to convert .j3o to .blend?
No.
so how can I editing ( remove some unwanted edge and faces ) a j3o file?
You can’t. There is no way to convert a .j3o file back to .blend.
I don’t get the point why you would need that anyway… If you need to edit your mesh, use Blender not jME for that and export it again 
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I can’t, because my mesh is made by navmesh Generator and I need to edit it.
Ok, then you should try to tweak some settings before generating the navmesh. Do you need to generate the mesh dynamically?
However, there is no built-in way to re-convert a j3o to blend …
The closest your going to get is to write a j3o to obj converter, which wouldn’t be all that hard, then import the obj to blender.
yes and I made it in runtime. and I want to remove shapes that are on top of my buildings model and connect some disconnected islands together…
Okay…
You could go for @thetoucher’s solution.
I don’t know if that’s possible but what if you redesign your scene and separate your islands within different nodes and generate the navmesh for each of them (separately)?
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how can I convert j3o to obj? is it possible to use jme sdk to do that?
or in writing mesh on disk I can export to obj?
You will need to write a class that takes the mesh object, iterates over it and write a new obj file using the following as a reference: Object Files (.obj)
to my knowledge this has not been done yet, you will have to write all of it.
I think you should take a big step back however, I think you would be better working on a new way to generate a more accurate navmesh, rather than trying to change what has been created. I don’t know what this method is.
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I separated traversable area in node(terrain and buildings and trees and roads ) but at the end I cant remove top of the building by changing navmesh generator parameters…
so I need to remove them manual.
The answer to your question is what @thetoucher recommends, but the solution to your Problem is really what @Domenic says.
The thing is: Editing a Navmesh will fail in most of the cases. This starts that you have two meshes to edit usually (detail mesh and nav mesh), you can break everything if you remove connections in the wrong places and that the generator should in theory just be tweaked:
E.g. the islands on the buildings, I don’t know if they aren’t removed if the agent can’t reach them (that means settings like agentMaxClimb), but it could be that they stay in case of off-mesh connections (teleport). But actually having this doesn’t hurt as there is no connection to the top of the building anyway.
Another way would be to remove the roof of the nav mesh (e.g. in my game, I could mark them with userdata as no_collission, so they don’t go into the navmesh at all).
For connecting the islands, try playing with the cell sizes (there is a reason why they didn’t get connected)
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