Happy Days/WMG

Chuck was an early version of Dawn from Buffy the Vampire Slayer
The monks, before lucking out in the early 2000s by finding a Slayer with a family, frequently incarnated the Key, moving it around to keep Glory from tracing its energies. In this instance, it located them within a humdrum family situation with an associated member who may have had some kind of latent mystic powers. But as Fonzie's rep grew, attention began to be paid to that small section of Milwaukee. So it was that one day, when Chuck left for school, the spell was reversed. Only Fonzie retained any memories of Chuck, describing him to Al in a flashback, although Al must have been confused when Howard denied ever having known a Chuck. Finally, even Fonzie lost these memories as he rapidly filled Chuck's place in the Cunninghams' lives.

Chuck did more than just ascend the stairs...
He Ascended to A Higher Plane of Existence.

Fonzie killed Chuck.
In order to become a more powerful Ensemble Darkhorse, Fonzie had to get rid of Chuck and take his place. Breakout Character? He forcibly made himself one.

Chuck's still in his room.
Due to not having a lot of screen time, brother Chuck may have suffered from some kind of mental illness the audience didn't get to know about. This being The Fifties, the stigma may have been great enough that Chuck voluntarily withdrew from society, or his family kept him upstairs to save face.

Fonzie is a Ta'veren male channeler
He used Balefire on Chuck to pull him out of the Pattern. He also uses channeling to get the jukebox to play.

Fonzie is a Technopath.
The Fonz has shown repeatedly that he can pretty much make any device work by either tapping it, punching it or even just clicking his fingers. If you check out the Technopath trope, you will see that Fonzie fits this trope quite well.

There is some sort of Worm Hole in suburban Milwaukee.
Hence the '70s-style hairdos and attitudes seen in the late '50s-early '60s; the gang were continually slipping back and forth about 20 years. About 20 years later, it manifested again in the nearby town of Point Place, causing one Eric Forman and his friends in the late '70s to occasionally act and talk more like the cast of Friends.

Chuck Cunningham was taken by Mork.
He then altered everyone's memories so they never missed him. Chuck mentioned his brother Richie a few times. This explains why Mork decided to visit Richie of all people on Earth and take him back to Ork.

Chuck was absorbed by a Doctor Who style space-time rift in the Cunningham's Attic.
It explains his dissapearance and the cast forgetting him perfectly!

"Roger Phillips" was SUPPOSED to be a returning Chuck Cunningham, but Garry Marshall called an audible at the last minute.
The more I think about this one, the more sense it makes.