(Bug) Unbreakable invisible object after erasing mods

I recently deleted almost all of my mods, only one of which contained any new items. After I deleted all of them, I went back into my game and realized that a small ornate bookcase was missing from my ship. It would have made more sense if the item had been from a mod, but the bookcase is a vanilla item. After a little while I realized that whenever I jump on top of where it used to be, the game thinks I am walking on top of a physical object. I looked at /boxes and sure enough, there is a red line right where the top surface of the bookcase was. I would be more tolerant of this if I didn't want to put something there, but I just want the bookcase to be visible again. Is there any way I can fix this?