Even though the characters in Rise of the Runelords have the same name and class as the characters in the the class decks, they are not the exact same characters.
Differences in feat progression, as well as deck lists, and especially character powers, are intended.
For every class, Paizo regards a certain character as "iconic" -- the de facto representative of the class. (See the paizo blog).
For the first appearance of a class in a PACG set, you are going to get the iconic character. And, the class deck for that class is going to have the same iconic character -- but no one wants two characters that play exactly alike, so everything is tweaked.
Switching to a class deck character is just like switching to a character with a totally different name -- you're playing a completely different character. Note that the class deck characters aren't "better" than the base set characters (at least, not necessarily) - they're just different.
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To expand further, normally you wouldn't switch characters during an adventure path, whether to a different version (e.g., Rise of the Runelords Kyra to class deck Kyra) or to an entirely different character (e.g., Rise of the Runelords Kyra to class deck Zarlova).
You're describing an exceptional circumstance, however, so if your group wants to switch from the characters they've been playing to the newly available characters, I don't see any reason why you shouldn't do it.
If I were going to do this, I would simply apply the number of skill, power, and card feats that each starting character has earned to the replacement characters. Then I would keep any of the cards that fit into the replacement characters' card lists (e.g., anything that class deck Kyra can keep from Rise of the Runelords Kyra); then place all of the remaining cards into a pool. Replacement characters (and only replacement characters) may then fill "empty" card slots with cards from the pool, but aren't required to do so (this will allow your party to potentially keep some useful cards that have been earned during the adventure). If replacement characters still have "empty" card slots, use the standard rules for rebuilding decks (see the Between Games section of the rulebook). You should end with each character advanced appropriately for the adventure path, as well as complete decks.
As alternatives, though, you may consider either starting over with new characters or finishing the adventure path with the current characters and then playing again with a new batch of characters. The replacement method I've described sounds good on paper, but the reality is that a character's performance is tied to the character's rules, so Rise of the Runelords Kyra won't perform in exactly the same manner as class deck Kyra. These variations in performance can affect the party as a whole, including which boons are acquired and retained in between games. This is where the games in the series have significant replay value, with different characters and combinations of characters, not to mention the random location deck compositions, providing different challenges.