I gave it a try but couldn't get it to work. First I set the sprite to 0 and then changed the other sprite to cylinder. No luck.
So then I tried setting the sprite to 0, saving and exiting the emulator, reloading, and then changing the other sprite to cylinder. The thinking being that maybe some variable or flag was being stored by the software that could be cleared by reloading. Again no luck.
Finally, I renamed the .3dn file and started with a fresh one thinking maybe the file was storing a value. No luck there either.
I tried in multiple different spots where I know the problem exists but couldn't get it to work. I even found that the sprite serves another role by being pieced together to form giant letters in one instance. Parts of the letters were missing when I set the sprite to zero.
Here's another thing. I must be wrong about it being just overlap because sprites overlap all the time in these games and it has never been a problem, but also I found a spot where that sprite didn't make this happen as well. I'm going to play around with it some more and see if I can find out anything else.