Reference tree shows two roots?

Here’s an image of my reference tree when I right click on my game folder, and click reference viewer:

At one point in time, my current save failed, so I went into one of the autosaves and began to work from there. I re-saved the map as TheOldHollow, rather than TheOldHollow_Auto1, and went about my business. I’ve recently been running into quite a few crashes while working on this map - 15-20 a day - and I wonder if this has something to do with it. Any way I can redirect those references to the external map?

This appears to show all current maps in the Maps directory - wish this was a little more clear, but this hasn’t been an issue.