Here's how AWC work:
When you recruit a new soldier with AWC already built, the game rolls a hidden ability with a specific rank requirements for that soldier; or when you built AWC, it rolls for all your existing soldiers; Then this part starts to cause problems, those hidden abilities only get revealed when your soldier lands on EXACTLY the required rank of the hidden ability (this is not the rank of when you get the ability for the original class, just a random number generated by AWC), so if the required rank is lower than the soldier's current rank, tough luck, the soldier has lost his opportunity to get a bonus perk FOREVER, unless you rebuild AWC then it rerolls everyone's perk but it's not ideal either (you need to keep rerolling and building takes time).