OK this is going to be really stupid, but I have made a new clean plugin I named Helgen Rebuilt Rebuilt. (Fate has a sense of irony it seems) And I have it checked as active and a check in the box for my other plugin I want to get the data from. It's loaded, and I can see all my stuff, but how do I now copy what I want and save it in the new plugin?
Any edits you make to anything will be saved in your active plugin. When I did it, I had a new cell so I selected everthing and did a Cut & Replace. Everything was then "edited" and saved in my new plugin. (Remember, you can select things in the Cell View, which made it pretty easy for me.
I figured I'd help you find the problem, maybe someone else has a better solution for fixing it

I was hoping Arthmoor would have a way to deal with the CELL record problem so you'd just lose the navmesh.