There's some interesting theories out there that Phillip Jeffries was not on the phone with Cooper telling him he had to come back to the Black Lodge, and that it was Mike Gerard instead. To early to suspect this. He does show up in FWWM, and maybe he suffered the same fate as Briggs? Or does he have a doubleganger wreaking havoc with Cooper?

Windom must be around somewhere. At the end of season 2 Bob took his soul, but that doesn't mean he isn't doing anything with it....

So much to consider! I'm just glad Twin Peaks is back!