First post...
Actually, this sinkhole is not permanent. It can be solved by the God Mode tools, however, in some cases it is extremely difficult to fix it because the radiused leveler seems to only affect a certain point of the tile. You may have to rotate the views or put the cursor over different tiles to find the position where it will affect the hole.
For me, it has happened two times, and both times were when I was on very low ground, near sea level. I wonder if that could be a factor in creating the hole...
Chrno.