Have you tried viewing your city on ElvenArchitect? Sometimes that helps.
I had a similar situation last week. I lost a mana plant (not the same value, I know) and I was really annoyed. I wasn't going to try to recover such a small item but I couldn't figure out how it disappeared because I was in move mode, not sell mode, just rearranging. Couldn't figure out how it could be gone. I looked and looked and picked up stuff to look behind. I searched the whole vicinity/quadrant thoroughly and was eager to get home to view the architect (I was temporarily on mobile and architect isn't completely mobile friendly yet). I found it. It was sitting on a tile clear on the other side of the city. I still don't know how it got the heck over there. In my rearranging, I was only relocating it three tiles away when I lost it. Weird.
Good luck
I hope you find it was just hiding really well