If the writers even deal with it, it'll be dismissed. Rachel and Phoebe'll decide that they like living where they're living, and they'll just say, "Thanks for fixing the apartment, but we don't want it." I think that they like having all the characters living so close together.
I'm willing to bet that this was a possible outcome. They're married, they're roommates. Ross files for divorce, but in the end, they fall back in love with each other, so they have to stop the divorce before it's final. Alas, it never happened.
I'm betting this story will be completely dropped, along with Joey's boat. They'll stay where they are, and we'll never hear about it again. I'll admit there are a few funny Rachel and Joey stories that can still be done, but I really see no point in Phoebe living with Chandler and Monica.
That was most likely the original plan. If I'm correct, in the original 605 spoiler Ross and Rachel were supposed to stay married for six months before they could file for divorce. That would have changed the whole focus and direction of Season Six.
Also, since many Season Six previews made such a big deal about Rachel and Joey living together, I'm guessing it was originally supposed to happen earlier, and not near the end of the season. The writers don't plan THAT far in advance. Rachel would have probably moved in with Joey around Christmas when "Denise" came back. (I don't care what people say; I believe she existed at one point. Look at Phoebe's reaction to Rachel's Santa Claus comment in 603. She seems genuinely concerned.) So, we would have had a half season worth of Rachel/Joey stories before she "found a home" at the end.
I assumed when the writers dropped the marriage storyline, the Rachel "finding a home" storyline was dropped as a result. It could still be brought back after the writers get tired of Rachel and Joey, but it's way too early to tell.