I had the same problem a few days ago It was like it was stuck
where the hub initially saw the device but I tried doing some other settings so removed the Xbee and then tried re-pairing it but it didn't finish pairing and then hub would not see the xbee but when I did a scan with my other connected xbees they saw it connected to the hubitat network even though Hubitat didn't see it.
not sure if using Xtcu to recover the xbee and rewrite it's firmware fixed it or setting the problem xbee to an end device and then re-pairing it fixed. After setting it to an end device and re-pairing it to Hubitat. Hubitat could see it then. I could then remove it from Hubitat and reset the xbee setting back to a router and pair it again to Hubitat
I would try the recovery firmware option first.
end devices settings and a few I have also adjusted to attempt improvement
NJ = FF (to extend the joining time might help so device pair to them first)
NH = FF (maybe so devices could travel farther by going through more routers)
AP = 0 (for an end device)
SM = 1 (has to be not 0 for end devices)
of course to pair it after writing all the settings remove power from the xbee then put the hub into pairing and repower the xbee.