From Stu Tierney of TFJ (FWIW):
"I have in that past asked a Naniwa and Shapton representative about flattening. They both said straight up that one should use loose grit (that they both make and sell for the purpose) or a diamond plate (which Shapton can supply at huge cost, but undoubted ability). I asked specifically about sandpaper.
Mr. Naniwa sucked air between his teeth, said he'd heard about it but couldn't condone it. Said contamination was a real risk because (I thought, since been confirmed and expanded) of the way the sandpaper works against the ceramic type stones and how it's put together. Apparently the adhesive can contaminate the stones (little evidence, but it does exist. I thought this was the sole reason) and the abrasive in the sandpaper can grab and embed in the stones since it's been ripped out of a fixed position.
Mr. Shapton said in no uncertain terms "that will void the warranty". Also explained in a clipped manner the same thing that Mr. Naniwa said, it can contaminate the stones.
I spoke to these two at an event at my local large home centre.
Since that time, I also asked Mr. Saito (Sigma Power president) over tea and cake here at home about how one should go about flattening stones, and he said either a flattening stone, loose grit or a diamond plate, and Sigma Power can provide all three. He also explained how they all worked and why they work. Loose grit tends to 'roll' and breaks the binder down without doing anything to the abrasive in the stone. Flattening stones are based on a much stronger binding agent than the stones they're meant to flatten, but are mostly the same stuff. These flatteners should break down slower, and they will abrade the stone's abrasive and binder, which is a different action to loose grit. Because these flattening stones are hard, any dislodged particles will start to roll and even if they gouge the sharpening stone, they won't likely embed (and are usually large and easily spotted). Diamond plates work in a similar manner to flattening stones, but the binder is much stronger and the abrasive in them (diamond!) is much harder. Diamond plates will abrade the stone and binder, but won't easily let go their own abrasive and if any is disloged, again it will roll and is not likely to embed in the stone.
Again, I asked about sandpaper. He laughed, saw I was serious and explained in detail what actually happens...
Unlike loose grit on steel or glass which rolls on a hard backing, flattening stones which are hard and durable or diamond plates which are also hard backed, there is give in the paper, which means that a loose abrasive particle can be pushed into the paper and stay there until it's either worn away or finds a spot in the stone where it can solidly embed, as the paper isn't tough or durable. That little particle stays in the stone, and you'll need to actively remove it (unless you get lucky and it dislodges by itself). At the same time, worn paper tends to have less well held abrasive particles, and you also expose an alien substance to the stone, the adhesive that holds the abrasive to the paper. I kind of wonder how much of an effect this will have, but apparently because it's soft it will embed into the stone, and can be worked into the stone so it stays there for longer than it might otherwise do. You'd need to aggressively remove a layer of stone to get it out. At the same time, I showed him on Norton and King instructions where they said "use sandpaper" and he explained that because these stones are softer, anything that does embed isn't going to be staying put for very long, and any adhesive is unlikely to adversely affect the stone because these stones are softer and small areas of inconsistency are only going to have a short term effect on sharpening. They'll either be missed (not felt) or will work themselves out quickly. On harder 'ceramic' type stones, any foreign matter is less likely to 'fall out' or be worked out without the user's knowledge.
This was mostly what I'd already thought, but he explained it completely and thoroughly without any shadow of a doubt. He'd also spoken to some people who had indeed experienced contamination issues and the general consensus is that it doesn't happen often and when it does happen it's more an annoyance than a game killer, but when your job is sharpening, anything that upsets your routine is frowned upon and there's no advantage at all to using sandpaper over and above loose grit/flattening stones/diamond plates.
All that without getting into the point of some stones might be flat when dry, but change shape when wet, so flattening should be done when the stone is in 'ready to work' condition, not dry and not after sharpening. Interestingly, the 'no soak' Shapton Professional series are notorious for changing shape when wet...
And that's it. I've known for a while that sandpaper wasn't such a hot idea, had it confirmed from two sources and fully confirmed from the last.
If you use sandpaper and you're happy and you get no trouble, great! I'm happy for you. If you run into trouble, then the above is the likely reason why you're having trouble.
And it's not like proper flattening stuff is prohibitively expensive. Some sandblasting grit and piece of old glass is just as good as a proper, pukka kanaban and brand name flattening grit. I give the stuff away (grit only) it's so cheap (actually King brand at the moment) and I sleep well doing it knowing that the loose grit will be used and will not cause any undue troubles.
Yeah, I use diamond plates. I can afford danged near any plate I wish and use what I think is best. I won't tell anyone they need to use the same plate I do unless they're specifically asking me what I use and why I use it, and even then there's no need to use a diamond plate, loose grit is fine.
This isn't something I've taken up as a crusade to wipe out the use of sandpaper to flatten stones, but the reality is that it's not a great idea and it's not recommended by the folks who make the stones or use the stones (except for King and Norton). There's a better way to do it, and in the end it's cheaper than using sandpaper."