Y'know, it's funny. The only changes after the crossover for Mega Man are being Wily has a different story during #23 and, like everyone else, no recollection of the events during the Genesis Wave, and the third alteration is that the damage Break Man caused was undone.
For Sonic, however, it's a different story. Here's a timeline I made:
And this is what the BumbleKing member "Penguin God" said:
"Sorry Sonic, but 'the rest of Chuck's family' was Naugus'd."
"Sorry Sonic, but Silver's team was time warped."
"Sorry Sonic, but half the Grandmasters blew up for reasons."
"Sorry Sonic, but the Council was booted to go back to the monarchy."
"Sorry Sonic, but those feline ambiguous things and half the Wolf Pack wiped each other out."
"Sorry Sonic, but Charmy's better half decided to be a stay-at-home mother."
"Sorry Sonic, your doctor transferred to another hospital."
Just proves my point that playing it safe would be lazy.