That was the same issue I was having... I thought it was just on my end. Here try this, it seemed to work for me. Instead of just hitting 'save' when you overwrite your old save file on your computer during the extract proccess. Actually click on the old save and overwrite it that way. Not just the name, but make sure the icon is highlighed etc. When I started saving like that I had no issues with the editor at all.
Note that you will not get more skill points for releveling. 49 is where it caps. You'll also gain exp normally so if you want to stay at a low level you'll need to downlevel again every so often.