Retraining generally takes a week of downtime. And you have to have found someone to pay to help you retrain. In some Adventure Paths (APs) there is enough downtime to actually make this viable (I'm looking at you, KingMaker, which had months of downtime). I'm not really seeing enough downtime in Wrath of the Righteous (WotR) to make this work.
Here is what I propose:
The PC makes a declaration to the GM/table that they plan to retrain out of X and retrain into Y.
Immediately, they lose X.
After a week of in-game time, they make a skill check (generally the DC of which is the Hard DC for the level of Y):
Critical Success: They can immediately begin using Y with no penalties
Success: They can immediately begin using Y, but with a -2 Retraining penalty related to using Y. This penalty goes away after one week of in-game time.
Failure: You still have lost X, and can immediately start a new week of training into Y
Critical Failure: You still have lost X, and must wait an in-game week before restarting training into Y.
For instance, if Harry the level 8 Rogue wanted to retrain out of a general feat taken at level 3 and replace it with a level 2 feat, then the DC would be 18 (16 for level 2 and +2 for Hard DC). If instead it was being replaced by a level 7 feat, the DC would be 25.
If Harry's feat was a Thievery-related feat, then the applicable skill would be Thievery. But, if the feat was related to something else (let's say Toughness), then the applicable skill would be different (in Toughness' case, it would be Fortitude). Non-obvious applicable skills would have to be discussed with the GM.