I'm no expert in this area, but my experience with sealants for our travertine shower and trowled concrete (not stamped, but similar, to provide a look of flagstone) has me say the following (my responses in bold):
Quote Originally Posted by cschnurr View Post
Do the deposits form under or on top of the sealant.
Probably on top though sealant isn't just a literal seal on top, but absorbs a bit into the concerete or stone sort of like multiple layers of defense in keeping water out.
If under, does the sealant need to be removed in order to wash away the deposits?
No, especially not if you use acid due to the acid's partial removal of the sealant (see below).
If on top, does the muriatic acid damage the sealant?
Sort of, in the sense that it will partially remove it. Your particular sealant has acid and alkali resistance, but a strong enough acid will still attack it. Generally "stripping" before resealing (aka acid etching) uses 1 part Muriatic Acid to 4 parts water (i.e. 20% diluted Muriatic Acid) and you are going to be using 10% so I would expect that you would need to re-seal after you are done removing the deposits (and of course, thoroughly rince the acid away after it has removed the deposits).
This might be one of those times when seeking a professional to do the works makes more sense -- especially if they take responsibility for anything that goes wrong.

Richard