I have a game added to my steam library a long time ago (I redeemed it with a physical retail CD-key, let's call "XXXX") and then I would know what happens with this retail cd-key if I buy a steam key ("YYYY") of a pack collection of various games that includes this same game that I had redeem with a retail CD-Key, so then after activating this pack will I have the same retail CD-Key still for this specific game (the "XXXX"), or it will be changed for other different key ("ZZZZ")?
As you know, CD keys can only be used once (or deactivated before it is used, from the developer's side). Once used, they'll go into a list of used keys, where it'll be eventually (after a very long time^) be reused.
If you apply a new CD key containing a subset of games and you own copies of one (or more) of the games you have already owned is in that bundle, you do not get a second copy, or a new CD key in replacement to the old one.
All you get is the remaining games (and DLC's) in the bundle that you do not already own that the key grants.
However, there are exceptions to the rule but only apply to games purchased from the Steam Store, and are granted as a Steam Gift (item).
^Open to speculation