Note: Show History is a Netbeans Feature (like a Version Control). The j3o only contains the latest Version. Your are not seeing history for other models because you probably didnt change them.
One could however use that to export different versions and maybe have a look with a hex editor.
I have found the problem 
it’s a problem with terrain controls, if I fix it I will make a PR with fix.
That was quick, thanks so much! Now I can finally get back to designing the worlds and maps and hopefully have the first version of my game finished up soon 
You’re right I was totally wrong about that, I didn’t know that was a netbeans feature. It looked like it correlated with this issue so I got excited and thought that was possibly the cause 
but I guess that was just a coincidence