So the recently released FAQ clarifies that "after refresh" actions happen after step 3 of the refresh phase. This means they happen before the action window opens correct?

MasterJediAdam said:

That is correct. Note that they also errated two of the "after you refresh" cards to "after your refresh phase" which means those 2 cards trigger after the action window.

That is what I understood. It was unfortunate that I was on the action window side.

And remember because of this, Fleeing the Empire does not work if you reveal it as one of your first three objectives on your first turn since you skip the refresh phase.

Rogue 4 said:

That doesn't seem right. The rulebook says:

2. Refresh Phase
The active player takes the following steps in order:
1. He removes one focus token from each card in his play area. (Any effect with the text “after you refresh” can be used after completing this step.)

Exception: During his first turn only, the LS player does not take this step of the refresh phase.

So they only skip the first step of the refresh phase, not the entire refresh phase, so Fleeing the Empire does work on the LS players first turn as the Refresh Phase does occur, it just skips the remove focus token step.

I stand corrected, thanks for helping me realize that!