2 things here: If puppeteers are unavailable due to the other film, then we'd clearly have them loop some scenes here and there. Or, they'd film the scenes with those characters and performers on days they aren't filming the other film. Of course, the only big players on both would be Steve and Dave.... and maybe Bill, if he's going to be recast as any of Jim's characters...My fear over the casting is the upcoming new Muppet movie may conflict, no? That would leave a couple major Fraggle players without their performer if that were the case. That timing may play into this...
The other thing to consider... we know this film is pretty far down preproduction... a little hold ups here and there. What we don't know is how far in preproduction the other Muppet film is. There could be a chance that FR could get the green light ahead of the Muppet film. Plus, I'm sure they can film these back to back.
Wonder if they're going to film any of this in Canada, like the TV series was. Then they'd be able to get some of the Canadian puppeteers back as well.