In my head they never separated. Ever. Not in this universe. All that silly bull about them splitting up was just to get ratings for their new show.
They are still together. Now what we really need is a decent Muppet show, not that other one they tried to make.
Apparently Jim Henson planned on the two to break up, even announcing it publicly with the intention of doing a publicity campaign called "Pig in the 90's". The break up announcement was 6 days prior to Jim Henson's passing and was of course over shadowed and then dropped altogether as if it didn't happen. I think this is why their relationship status was muddled for a while.
I really would have liked to see how this campaign would have played out. True female independence was a big topic in the 90's. The Vice President criticized Murphy Brown for being a single mother. It makes sense for Piggy to flex her independence and focus on her career more so than the frog. I think the idea was perfect for the time, but sadly never came to be fully realized.
I think the problem is the latest break up was sloppy. The 2011 movie drops the bomb on us that they broke up around the MTM era (not specifically said in the movie, but based on the clothing and hair style of Piggy and novelizations). Then they get back together in the end because Kermit realizes Piggy won't chase him anymore and he has to admit he needs her as much as she needs him. I thought that was done perfectly for the movie. Then they continue to be together in MMW. Then they break up the characters AGAIN? That may have been the quickest rehash of an idea ever.
In the 2015 show they turned the break up into a weird petty relationship of the two getting back at each other. Then Kermit has a realization after Piggy says she love him before surgery? I mean.... the whole thing was done far worse than the 2011 movie where the characters seemed far more mature than the "mature" audience show.
To me this is the issue with the Muppets. No one is really steering the ship and they keeps changing course. They need to have someone who is in control, creatively, for all Muppet productions. Someone who ensures that all productions keep the characters true to form and follow certain guidelines instead of allowing for vast shifts in characterization.