Not too sure about this, haven't messed with channel to flow much, but couldn't you just use the ore.exe or granite.exe to rewall it then just min it out again? It'll take some time, but I think its the only way to really fix this. Unfortunately I think you'll also lose whatever items are on the square...
Edit: Sorry, misread your post. Still, you should be able to rewall the square and mine it out, not sure if it'll delete the item or just drop it on the ground, but there ya go.
Edit 2: I also just thought of something about this. There's a very good chance it'll crash your game... Try setting up a test game and rewalling over an item on the ground and see what happens.
[ June 16, 2007: Message edited by: Lord_Daeloth ]
[ June 16, 2007: Message edited by: Lord_Daeloth ]