"The number of tile columns has changed" popup keeps coming up, even while we've already clicked "Yes" #1770

It appears that Tiled incorrectly remembers you have already changed the number of tile columns.

I get the "The number of tile columns in the tileset 'XXX' appears to have changed from XX to XX. Do you want to adjust tile references?" every time I open my .json map.

Clicking "yes" on it the first time does update all of the tile indices correctly, but using it a second time actually breaks the map again.