I went to cook and came back to it later in the evening and it was fine again. I guess it just needed reloaded. It was the oddest thing I had ever seen in Valheim, given that I rarely see any glitches in Valheim.

I should have gotten a picture of it before I left the game. It was frustrating but funny at the same time. If I would have thought, it would have been a neat way to add some storage so just the lid of the chest was above the floor.