Yeah, I'm really sorry to say it, but Elias, Finitevus, Mina, Geoffrey, Moggul, Lara-Su and everyone else is gone. Chances for their comeback are really slim.
1 Archie won't pay Penders. It would be really uncomfortable for them to have another guy (next to Sega) telling them what they can or can't do.
2 It's too late. Reebot happened, some characters took place of old ones. Making another reebot, keeping both casts, would be very hard to pull of.
3 Even if Penders gives him characters back, Bollers, Gallagher and the rest could sue Archie again. Too much risk.
4 Sega doesn't really gives a damn. Did they ever help Archie in any way (Ok, once. They didn't allowed Penders to kill Sally in issue 50).
5 Like some people pointed out, sales are better now (not 100% sure on this one. Also one can argue that second reebot five years from now could help sales again).
So yeah, we have to deal with it. Our only chances is that Archie will find those documents that prove that they own those characters. If not, game over.
I'm more focused on who survived. We know that Hood and Akluth (Flynn characters) stayed. So I mostly think about 6 characters:
1 Scourge (he's... complicated)
2 Shard (writer who made him, didn't created 'Shard', just another Metal Sonic)
3 Boregard (made by Flynn, but was references in the past by Bunnie)
4 Conquering Storm & other brides (they have a lot ties with old universe)
5 Matilda (same deal as Boregard)
6 Trash (technicly 100% Flynn character but... what he suppose to be now, all echidnas are gone!)