I have done the same thing, I have heard you can sharpen/grind out the damage, but the stop has to be changed when you do that. Look around for articles on sharpening bonsai tools, I haven't yet so if you find something good, please share.
I actually came across those videos a while back on youtube and found them extremely useful when learning how to sharpen my tools.
I also found a website that offers a service of sharpening and realigning tools. There were a few pictures showing their processes and I figured my knowledge of knife and axe sharpening should transfer over. I managed to file the blades and realign them. Now they're better and sharper than ever.