My theory about how this goes down.
ENT-TOS-TAS-TNG-DS9-VOY (old Trek)
timeline leads into Temporal War. A Romulan goes back in time and delays the Eugenics Wars from the 1990s to the 21st century. Sera is posted on Earth since circa 1992.
new timeline.
ENT-Disco1&2-SNW-TOS-TAS-TNG-DS9-VOY-PIC etc. (new Trek)
Romulans still angry the Fed forms anyway. This time they send another mission to go back in time and blow up the Noonien-Singh Institute's reactor to kill Khan. The Fed fails to form and leads to Wesley Kirk's United Earth timeline.
Fed Temporal agents are immunized from the changes and still remember the Fed. One goes back in time to tell La'an to restore the Fed, gives La'an the time device, and dies in the process.
Events of Tomorrow and Tomorrow and Tomorrow
La'an saves Khan and the Fed is restored. Since at least new Trek started we've been in a "close enough" timeline:
https://tvtropes.org/pmwiki/pmwiki.php/Main/CloseEnoughTimeline . Old Trek is still canon in broad strokes (we now have to ignore mentions of 1996 in Space Seed and Wrath of Khan, we probably have to pretend old Trek's 1701 always looked super-advanced, etc.)
I've always thought it was improbable that Mirror universe/Kelvin timeline etc. would still have the same people born as conveninent counterparts to the Prime timeline characters, but we rolled with it. However, in light of TAS and SNW I might theorize that Robert April literally is a genetically different person now because of the timeline changes.