There is a good chance that the stone does not need fixing. It looks like it is a crack in the stone, and not a protrusion. In that case, your finger might feel it, but the steel would just float over it with no damage. Look at it carefully with your magnifier. I'm betting it is not a problem.

The hardest part for me was to learn to throroughly establish the bevel. Make sure you spend enough time on the 1k before moving on. Check it well with your magnfier as you progress. Also, make sure that the entire edge is thoroughly set before going to the next stone.

Perhaps also a good idea, as a means of learning what the different parts actually do, to shave off the separate stones. You should certainly be able to shave off a 6k stone. Then add the chinese stone, then finally try with the paste. You can do the same with stropping. This might help you experience what the different hones actually add to your honing routine.

Best of luck.