I mean, I guess it depends on how experienced the character is supposed to be as of the start of the adventure. I'm assuming you're working on a standard Strength/Intelligence/Charisma kind of thing, by the way.
Obviously, when going through a playable flashback halfway through the game at level 40 or whatever, stats are going to be vastly different from the flashback if it takes place, say, on the character's very first mission, years before the start of the game. But...my guess is that the character's stats at that particular mission and the character's stats as of the start of the game WOULDN'T be that far from one another, right? You're simply going from "inexperienced" at the start of the game to "complete newbie" as of the flashback...I would think just a simple percentage of stats would suffice.
Say, for example...
The player creates character Jack at the start of the game with 5 Strength, 4 Dexterity, 2 Intelligence, and 2 Charisma. Jack hits things real good but don't talk too good.
Halfway through the game, Jack is in a bar. Note that we don't give a single fucking shit what his stats are at this moment, because why would his stats now have any effect whatsoever on a flashback? He's retard talking his way through a conversation with a random barkeep, and the player, through your dialogue tree, sets up a situation where Jack, on his first mercenary mission, went up against a small band of thieves to save a farmer's kidnapped daughter.
So you start a new scene: Jack as a complete newbie, years before the actual first playable scene in the game. Just make all of his stats here, say, 75% of his starting stats. Jack, as the newbie, has 3 Strength, 3 Dexterity, 1 Intelligence, and 1 Charisma, seeing as how he hasn't had time to build up his muscles and fighting skills up to the 5 and 4, respectively, that he had been assigned at the start of the game.
And as for skills (as in, like, Tackle or Double Slash or whatever)? He has fucking none. Because he's a fucking newbie. Or, if you'd prefer to go a slightly more humorous route, assign him a bunch of skills like Windmill Punch, Cower, that don't appear anywhere else in the game. You know, skills that he would rapidly have gotten rid of because they're worthless.
All in all? It's kind of hard to say without actually knowing what kind of stat system you want to have set up. I'm just making assumptions and then working off of those possibly groundless assumptions, here.