Yes. If you look at itasan18's video on sharpening you will see the classic result of sharpening these knives wrong (I love his videos on cooking, but wouldn't recommend his sharpening video to anyone). He uses what looks like King 1000, King 6000, and something else that I don't recognize, but he clearly does a lot of sharpening on the ura-side of his knife with the 1000 stone. If you look at his knife, the ura side has been flattened to the point that the concave back has started to disappear. The flat area of the ura side is nearly 1 cm thick - all the way around, spine-side and edge-side! This is the natural result of over-sharpening the ura side. As long as the knife came with a decent ura polish, as most do, then you should only have to hit it with a very fine stone, just to polish it up and remove the burr from sharpening the face side of the knife. Now if the ura is significantly damaged (say a chip in the knife is large enough that removing the chip results in losing the flat edge on the ura) then you will need to go up through the progression again to reestablish the edge. Otherwise, for normal sharpening, you should not be sharpening the ura side with coarse stones. Your goal should be to end up with something like this...
That image was taken from So's japan-tool website. I'd highly suggest going there and reading his "journal" on traditional japanese knives he has restored and polished. Lot's of great info.
http://www.japan-tool.com/hamono/Knife_Polishing/Knife_Polishing.html