So, my first play through I ended up finding "daddy" and Peeper attacked me. No biggie.

This play through, I ended up going through the graveyard and fighting the corrupted Scion first, where Peeper got killed. I reloaded to an earlier save, but now Peeper is just gone. The quest hasn't updated and the conversation with daddy just has him telling me to bring Peeper to him. I did some searching, but couldn't find how to restore Peeper. Any console commands I could use?

Try teleporting to Driftwood Square. I noticed he gets lost if you teleport with him following you. But going back to Driftwood Square restored him.

No go. I've teleported to the square (as well as many other locations) and no Peeper. I've even tried teleporting to my current location, but again no change.

OK, this is going to out me as stupid, but did you go back to where you first meet him? Because when I first did this quest, I didn't realize you had to click on him after you speak to the ghost of Big Marge and walked all the way to the Magicockerel, only then realizing that he hadn't been following me and having to walk all the way back to find him!

He does follow you if you talk to him. As so often I forgot to cast spirit vision and didn't even notice Big Marge's ghost. But if you go to the Magicockerel without getting your instructions from Marge, you have to fight a horde of void chickens. Not challenging and not rewarding, since they don't even add EPs and the Magicockerel is gone for good when the fight starts.

It's not a stupid question, but yes. I've already went back to the chicken coop, and no sign of Peeper. Good idea, though. I'm pretty sure the game is just glitched at this point, and the only option is either console commands or sending it to Larian to fix.

That's a bummer! Sorry this happened to you.