The comic ended (well, that arc ended) with a panel going back to Cho’gall’s hand protruding from the rubble in Ahn’Qiraj after the heroes had left, and his appearance during Cataclysm - hulked out with stony protrusions and extra eyeballs on his body, along with his one-eyed head possessing tendrils in place of a beard and and fin-like ears - reflects his transformation from being empowered by C’thun’s remains, so the circumstances of his return after being beaten by Med’an were set up.
Thus the battle between him and Cho’gall still took place, wherein Aegwynn gave her life to help Med’an win. Moreover the events that led to Kathra’natir inhabiting Meryl’s body - which is referenced in Legion - were part of that conflict as well. The comics and characters involved remain canon, except for Med’an properly being an actual Guardian.
As of Legion, becoming Guardian has been attached to a specific process involved with the Forge of the Guardian. Guardians of Tirisfal were able to retain the borrowed power for as long as they wanted (though prior to Aegwynn they’d all willingly surrendered it back to the Forge when their tenure was over), while the method of empowering Med’an basically amounted to several spellcasters simultaneously channeling their magical energies to him through a ritual, and that resulting empowerment ended once the ritual stopped, returning the power to the casters.
That said, they’ve remained hesitant to concretely follow up on Med’an since, so to some it might seem like they’re leaning into a complete retroactive removal of him. But as things stand, the cause behind a number of significant things would need to otherwise be reconciled if they decided to outright excise him from the canon. Including, as said, Aegwynn’s absence since that era, Cho’gall’s appearance in Cataclysm (in fairness they’ve also yet to explain why his AU self has some of his MU self’s Old God mutations along with the chest wound that his MU self received during the Second War) and Meryl Winterstorm becoming Meryl Felstorm, along with the associated reconciliation of Valeera’s demonic possession story arc, which was part of her involvement in Varian’s story and therefore is more difficult to just arbitrarily erase without basically eradicating what little backstory she actually has.