Here is my problem with the entire loss discussion:
I have a character. It doesn't matter what feats he has. It doesn't matter which PrCs he has.
What matters is that the moment his Dex (or Str or Con or some other ability score) drops below 13 (or some other number), he loses part of his current feat tree.
If not having the feat disallows abilities of a PrC or other class ability, then he suddenly loses those abilities as well (if you rule that way).
Plus, you have to decide which ones he loses and which ones he does not lose. If he is no longer eligible for the PrC, there is a decent argument that he would lose BAB, saves, special abilities, hit points, etc., etc., etc.
What a nightmare!
How can anyone construe that as being fun?
It is much simpler to just say, screw the WotC rule that if you lose the prerequisite, you lose the feat. I think they fubared when they came up with this rule.
And, screw adapting that rule to skills or PrCs.
Otherwise, you are just begging for trouble in your game. IMO.
On the topic of allowing alertness (or items) to be used as a prerequisite, if you blow off the stupid loss rule in the first place, then you might as well allow them as prerequisites for consistency sake. Again, IMO.