As a practical matter, it's challenging to match a stain on an area after you accidently sand back into it, but it can be done.  

before you sand the whole thing, my first try would be to get a better match.

to do that, if i was too dark, i would sand it light again and just be very careful (using a relatively dry stain rag) to build it back to the right color density.  you can also apply some stain beyond the sanded area (yes, on top of the epoxy around your blotch) to make the edge of the sand-through less obvious.  if it was too light, you use a relatively dry rag to build it up.

remember, when you put epoxy over it, it is going to make it look darker....so you have to kind of match it for what its going to look like after the epoxy is applied (which means it sort of doesn't match when you do the stain only...so it matches when you apply the epoxy over it)

if you can't, by approaching it more carefully, get it done to your satisfaction, you could sand the whole seat and do it again.  if its a seat, it may not be that hard.....just be careful to not sand beyond the mahogony ply into the core....or now you have a worse problem.   

as a last resort, there is always paint the seat and/or some kind of sticker over your blotch.....but i don't think you need to go there yet.

h