So I went digging through the taz transcripts tumblr in response to this because I legit couldn’t remember exactly what was decided about this.
Griffin explicitly states in canon proper that Magnus remembers his “life with Julia in Raven’s Roost” (taz ep 55), but they don’t address the Kalen thing again in the course of the Balance Arc. They do however discuss it in The The Adventure Zone Zone 2017, pertinent section copied below:
Travis: Uh, Griffin, I have a question for you that a lot of people asked, I don’t know the answer to, which is—
Travis: —you talk about in, um, Episode 59, like— Well, two questions. One, so Magnus has the new body, right?
Travis: And the physical stuff that he lost during [crosstalk] Wonderland is back—
Griffin: [crosstalk] Oh, does he still— Does he remember Kalen?
Griffin: No, no no no. I— you— so the way that I kind of thought about this, and you all— this is what fucked me up when you guys were like, “Oh, don’t get back in your body, you’ll forget everything,” is we were kinda thinking about it in a different way, in that I was thinking that like, your memories and the things that you remember kinda resided in your spirit? Or whatever? That was inside of the mannequin, and so when it was outside of your body you were technically dead, and so the voidfish didn’t work on you, and that’s why you were remembering those visions and all that shit. But like, I think your memory lived in your spirit, so when it got back in your body, just because your body was from a time before Wonderland, like your brain would still remember Kalen? That’s not really how I think about it. I— uh— and frankly like—
Griffin: —that moment was too cool to take away. So like no, Magnus doesn’t remember Kalen, ‘cause I do kind of like this idea of Merle and Taako having to go on this vengeance quest for this dude they’ve never met before. That we may not— which may not happen, but just like, I’m not gonna take that away.
Justin: [crosstalk] So, I’m gonna— I’m gonna call it right— I’m gonna call it right now, we’re gonna have— At some point, we’re gonna do a live show, and it’s gonna be a two-night— hunt— the hunt for Governor Kalen.
Clint: [crosstalk] Oh, man!
Travis: [crosstalk] I’ll play— I’ll play as Kalen.
Clint: Oh, that’s excellent.
So Magnus still remembers everything but Kalen.