Super #17 Arc had far bigger retcons to the series such as Gero stating #17 was programmed to surpass Cell until Vegeta broke through the GOAT of gates and the only plot thread it had to connect it to the Evil Dragons Arc was the use of the Dragon Balls (there's also Piccolo in hell, but you could have his final meeting with Galu being in heaven and it wouldn't make a difference). You could omit the arc entirely, have the Dragon Balls used just after the Baby Arc in an attempt to restore Earth and you'd have a far tighter narrative and far less plot holes for GT as a whole.
I'd still rather omit Super's entirety over either of them though.