The altar dragons actually respawn, it just takes some time. Perhaps do some fast traveling, or use Wait (but not at the altar). Many reports are that re-spawning takes 30 in-game days, but I've had locations take only 10.

I just tested Skyborn Altar. 10 days was sufficient for the dragon to respawn. I find it fastest to look at the date on the map screen at bottom right, add 10 for your target, and fast travel the longest distances to pass time. Markarth<->Riften is ~26 hours.

From my experience if you arrive too early you will have to wait all over again, better to load back before the arrival.