Technically, given the way the O:ZT storyline played out in the comics when Bobby was away from the team for awhile, it wouldn't be completely out of the realm of possibility for him to pull a guest star role in an adaptation of that story....the character infamous for distancing himself from the X-Men ages ago in the animated universe WOULD be completely off of O:ZT's radar when they came for the X-Men, meaning if long-in-place protocols developed by Xavier in case the team was compromised ended up activated similar to the comics...Bobby could get pulled in to lend a helping hand to whichever mutants the protocols put him in contact with...like Marrow & CeCe.
(I'm not really expecting Bobby to show up in the show again, tbh, but just saying. O:ZT is his most famous storyline from the 90s and if the show does end up doing a version of it, his lack of connection with the X-Men team in the animated universe wouldn't necessarily be that big of a hindrance, and in fact, given the nature of the storyline and how it unfolds, could even help sell it in terms of how he's able to escape O:ZT's notice initially).