This is my first time to experiment with the whole skill points glitch and everything revolving around the FLU. I followed the guide perfectly (except for messing up something with Carth, but who cares about Carth?), and after I rescued Bastila, I had several levels for her. I used the RLU for level 3-4, then FLU'd the next one to 14->15. When I was done, Bastila had everything that I had given her throughout the FLU process, not just the stuff on the last level! If I'd known it would do this, I would have picked better stuff! Now I have a level 6 Bastila with Improved Energy Resistance, Heal, Force Armor, Knight Speed, Knight Valor, and Force Resistance.
I'm now experimenting to see if I can replicate this.
All of that disappears when you reload an area, I had the same thing happen today when I gave bastilla her powers. It only seems to happen when they have a second level up after you finish the FLU I replicated it with Canderous when I got into Davik's estate.