The clone thing has never been referenced in other works beyond Riptide (yet). So while it is the clone in Abyss, we can't be sure if anyone knew or not.
I'm still hoping for part 3 (Undertow, perhaps?). I loved Crosscurrent, and Riptide was alright. I had a lot of trouble following it, mostly because of the clones:
a) I knew the characters like Soldier and the rest were clones of Jedi or Sith we knew from previous EU material
b) I picture characters when I read, and try and hear their voices when they speak
c) I was given NO DESCRIPTION of any of the clones until the plot twists 3/4 through the book.
As a result, I felt I couldn't connect with the characters, because I felt I should've known what they looked/sounded like, but had no idea.
Also: welcome to the forums! For future reference, we have a great thread for general Star Wars questions, over here: http://www.eucantina.net/forums/viewtopic.php?t=982&start=105
"I must not fear. Fear is the mind-killer. Fear is the little-death that brings total obliteration. I will face my fear. I will permit it to pass over me and through me. And when it has gone past I will turn the inner eye to see its path. Where the fear has gone there will be nothing. Only I will remain."
-Bene Gesserit Litany Against Fear