1. No, it's not how it's enforced in the CB. That would be a major bug.
2. No, it's not RAW -- explicitly RAW, when you retrain a feat, you can retrain it to any feat that is now legal. (and retraining to have two paragon feats at 11, etc is explicilty allowed by phb).
I think you're not using retraining in CB correctly; I do that sort of thing all the time. You can't, of course, if you going back in time and using earlier retrain options, retrain to things that weren't legal at the time -- but then, doing so without explicit permission of the GM (or playing in LFR, where doing so is legal any time you're levelling up your character) isn't legal in the first place.
My take on the OP's quesiton: No, if you're going by RAW, players only get one retrain per level, which must be used at the point you level up the character (though a common allowance is to allow it to be used at any time before you gain another level).
OTOH, I think much more agressive rebuilds are totally ok (including stat redistribution or even Lab Accidents where class&/or race change) -- but those need to be worked out with the GM and unless they really are seamless, worked into the story. You don't want to force someone to play something they don't want to play--even if it was "I thought I wanted to play this, but now I don't," but you also want the game story to make sense in the context of the characters.