What does this mean for Robotnik/Eggman? Did Maria and Professor Gerald get retconned?
No, they're still present and accounted for (albeit dead). So Eggman/Robotnik still has an implied family, but like Knuckles, they can never explore it deeper. If there's a newly released game which further explores his family tree, then by all means, they'll be allowed to depict them. But considering SEGA's current direction, I doubt that's ever going to happen.
I'll have you know Donald Duck has a very expansive family going back many generations on both sides, leaving out only Huey, Dewy, Louie's pop.
Scrooge McDuck even has a age of Death.
As I said, despite never really changing, some of these mascot characters were given creative leeway by their owners. This allowed others to play around with them and give them more depth.
Nintendo's Mario was once one of them. Prior to the infamous live-action movie, Mario was everywhere: from cartoons to comics. And the creatives behind the products were given permission to do whatever they wanted with him. But after the movie, Mario and other Nintendo characters have never appeared in anything else outside of video-games. Recently, they seem to be warming up a bit (what with Bowser appearing in "Wreck-it Ralph" and Donkey Kong appearing in "Pixels"), but I doubt they're going to be making another Mario movie anytime soon.
Sonic is another example. Like Nintendo, ever since the bad-reception of 06 and Penders' run on the comics, SEGA has gotten more strict with their characters since then, out of fear of another disaster. They haven't banned Sonic from appearing in other media yet, but you can tell any of his modern appearances are sticking closer to the official canon. The one exception, so far, appears to be "Boom", but only because it's a spinoff series commissioned by SEGA themselves. There's no telling what direction the upcoming movie will take.