I didn't wipe my profile when I updated to AE on my desktop, but when I got a laptop and put FTL on it, I kept the profile as new. So I am unfamiliar with unlocking ships in AE (v 1.5.13).
I just won with the Kestrel on Hard and unlocked zero ships. (I didn't play straight through.) So what ship should I have unlocked? Just the Engi A?
Pretty much. You've got to do the achievements and ship quests if you want more. Even Federation A requires a quest nowadays (Rebel Stronghold, Second Rebel Flagship quest.)
Although did you unlock Engi A when you hit Sector 5? Or not even that?
Apparently not. I remember an achievement pop up, but when I got to the end of the game, it's not in my hangar. So actually, a Kestrel win gets no ships?
I started with no mods. Does adding a mod (just Extended Fleet Pursuit) midgame wipe out a flag or something?
No, I haven't tried at lower difficulty. I may do that, if it still doesn't work. I didn't get any of the achievements to unlock the Red Tail yet, so there's opportunity. Or I may end up using the editor.
Follow up: So I got to sector 5 and got the Engi unlock. I wonder if there is a limit on pop ups. I remember getting the "Just Getting Started" achievements for Easy and Normal, but I don't remember seeing Hard. So maybe the Engi unlock didn't register?