FWIW I tried to do this with the character builder...
I did a quick build of a level 11 cleric and then went back and picked multi warlord at 4 and the 3 power-swap feats after that, and some random feat at 11th.
I picked new powers at levels 6, 8, and 10 for the power swap feats (the builder gives you the option to change them each level, in addition to whatever retraining you want to do, which is good because that's what RAW says).
I leveled up to 12 and visited the retraining tab, and pulled out Student of Battle for Acolyte of Divine Secrets. At this point, the builder was very confused. It automatically flagged my character as houseruled, marking the power-swap feats and their powers as house-ruled. I could not use the builder to swap the powers (I was able to take my own powers back through a non-intuitive means, but that's a usability issue not a rules issue
).
Even after taking my powers back, the feats were still house-ruled. (I tried unselecting them, bypassing the retraining rules, and reselecting them, as if I had made an error during the selection process, and it was still a house rule.)
Not saying that the character builder is the final authority on the rules, but it certainly things you need 4 levels of crap to deal with the retraining issues. I agree with the above posters though, let your character do it faster--over the course of a level even might be a good duration.