You could delete the map data for that region, and it would be recreated when you went there again.
Use a marker to write a unique phrase on an item and save, then search the save folder to figure out what map file that item’s in. On Linux that’s:
grep -l "unique phrase" save/WorldName/maps/*/*
If you’re on windows you’ll need some tool that can search files for a string.
It’ll find it in something like “maps/0.0.0/25.23.0.map” That’s the X,Y,Z for your current region, then square. Delete the ones where the second number is lower, and you’ll remove the stuff to the north. So you could delete 25.22.0 and onward to just clear a few squares, or you could wipe the whole 0.-1.0 folder if the bad spot’s in there somewhere.
There’s also the chance that you’ll get a read error or something when trying to search the files, and that’ll tell you where the problem is, too.