The easiest explanation is that Sagan 4, at this time, has higher oxygen levels. That alone won't be sufficient, though. Is there some kind of cladogram that shows the development of different modes of respiration among the Ukfauna? Basic respiratory structures could probably evolve convergently.
I believe clade-specific plagues specifically as a form of retconning should be used very sparingly. This is especially true for Sagan 4's Alpha timeline, since it's not meant to be as strictly scientific in tone as the Beta timeline.
If necessary, one could find the least plausible lineage and do a sort of "soft retcon" by making a genus group for them (only plausible if they're small) or a very widespread, generalist species that makes scientific sense, which also re-occupies the niche for most of them.
There is also a possibility of making a microbe or parasite of some sort that alters their physiology slightly. Perhaps some could have dense coatings of "algae" that produce oxygen for them, or gut biota which produce oxygen that is, in turn, absorbed by the gut lining. This would only work for the more borderline examples, though.
A extinction event that's an oxygen crash could wipe out implausible Ukfana by saying their sizes are no longer sustainable, although it would wipe out many other fauna, too.