Well, if seasons 4&5 are anything to go by, they tend to use the final seasons, even the final episodes as kind of metaphors for where the characters will end up in the next season.
So in the season 4 finale, for instance, Selina spends the entire episode in limbo before being fucked over by Tom James – which is basically the shape of her arc in season 5 – Dan is separated from the Meyer-crew, a separation he will come to embrace over the next season, and Amy calls Dan for help, but doesn’t get through to him, a missed connection which shapes HER arc.
As for season 5, it’s even more blatant. In episode 5.10 Selina’s story goes straight downhill with the brakes off, which is a pretty apt description of season 6. Amy blows Dan off, tries a relationship with Buddy, and ultimately leaves him for Selina. And Dan…Dan gets everything he thinks he wants.
So, yes, Dan going to rejoin Amy is almost certainly significant. (It was also probably good for her – she was almost a certainly a wound up nervous wreck at that point and, while I doubt they talked about it in the room, just having him with her would…steady her a bit).
I won’t go into Selina in 6.10, because I can’t predict where she’ll end up for the life of me, but looking at the episode as a whole, the meaning of Amy openly declaring that she’s going to leave Selina to go work/be with Dan – only to be interrupted by an inconvenient pregnancy – seems pretty clear to me (and a clear contrast with her leaving Buddy FOR Selina).
Of course Amy drops her pregnancy bomb and gets the hell away from him, expecting to be left alone, and then, after a short pause, Dan joins her. Which I think illustrates the shape of Dan’s arc for the next year – Amy might think she’s going to be abandoned, but HE knows he can’t do that.
What we don’t see, of course, is Amy’s reaction to him joining her – so it’s entirely up in the air how receptive she’s likely to be.