I haven't rewatched X-Men: TAS since childhood, which is the reason I haven't started watching X-Men '97, so I can't weigh in on this. A decision on how to handle it will likely be made once the season concludes. The Appendix has an editor who dedicates his time to the X-Men: TAS profiles (and there are many of them:
http://www.marvunapp.com/list/app92131.htm), so this topic is bound to come up sooner or later, I think
Here's my understanding:
Earth-13393 is Cable's future alone. This is a separate future, centuries after Bishop's timeline(s).
Bishop's timelines via 2055 are
1.
Earth-31393 = Sentinels rule the world due to Kelly's death. (Cable will exist but in his tangental Earth-13393 LONG after Earth-31393's time period.)
2.
Earth-121193 = The plague's origin is not 100% clear to Forge based on existing record but it's the virus' destruction that leads to a different type of plague that slowly wipes out mutants. THIS is where I think the confusion is in relation to Earth-13393, because clearly this has to be the timeline Bishop ended up in after saving Senator Kelly. (Forge is even like "Who are the X-Men?". Well they died before he could meet them therefore it's the same timeline by the end of "Time Fugitives Part 1".) - Cable's future CANNOT co-exist as a branch of Earth-92131 because of this, therefore he will try to prevent it.
3.
Earth-121893 = Bishop's new future after preventing the mutant-killing plague. Sentinels aren't as much of a threat to Bishop's resistance as they were previously. A fed-up Master Mold now wants to execute Xavier in 1959, creating a brief X-Men-less timeline aka Earth-95099 (before that's erased) - but also utilizes a trojan horse program in case of Nimrod's destruction, because Master Mold implemented him with nanites that would eventually birth Bastion and influence the future of Earth-121893 a few centuries after 2055 - but because that gets erased by
present day Bastion's demise yet
Bishop still exists even without his time travel wrist device on as seen in in '97 Season 2... (and as we know that's how Wolvie and Storm's variants from Earth-95099 died because they deactivated their same devices and the let the current timeline erase their existence)
Cable's future, Earth-13393 is the only potential future left. Previously, could co-exist with Earth-31393 and Earth-121893 from the 90s to 2055 to even centuries later (but BEFORE 2960) -
this seems to be the current future of Bishop as well.
So basically, if they kill off Apocalypse for good in modern day by the end of '97 season two...that will raise an interesting temporal paradox for not only Cable but Bishop as well. Maybe. That would be the thing to look out for to answer all these questions.
(Sidenote: The fact Cable and Bishop were able to survive past "Beyond Good & Evil" is evidenced later in the OG show by Apocalypse having a back-up Lazarus Chamber; thus fixing this temporal paradox because yeah. Despite Xavier saying Apocalypse "wouldn't exist" once plucked out of the Axis of Time ...he still had that one back-up Xavier didn't know about. Earth-13393 is still inevitable.)
