Prestige class and doubled feats

[radekw]

How to solve a situation when prestige class chosen by a player includes feats which he already has?
I assume that if such feat can be enforced it will, but what when it can not be streghten? Is it simply lost? Or maybe another one can be chosen instead? Or maybe player can change the feat he already have?
Thank you in advance for the answers and sorry for my English :)

[Yora]

Following the rules as they are written, the character would have the feat twice but with the same effect as if he had it only once. (Unless you can take the feat twice and apply it to different things of course.)

However, I think it is very common that players are allowed to take another feat instead. It is probably a good idea to limit that choice to a feat that is somewhat similar instead of allowing to just take any feat they qualify for.
For example when a character gets Endurance as a bonus feat but already has Endurance, I would allow the player to take Great Fortitude, Toughness or Diehard instead, but not a Metamagic Feat or Weapon Finesse.

[Gwendol]

In many cases this is spelled out in the class description, and for the other cases it will have to be decided at the table. Rules-wise, those will be wasted class abilities.

[Khedrac]

You can use the retraining rules (PHB2) to replace the original feat at the same time the character gains the bonus feat.
About the only place where this fails (I think) is if it was a pre-requisite for another feat already taken.