They'll pop up again. Chances are they're flying in the Depths.
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I’ve been waiting a loooong time, almost an in game day. I’ve also tried flying their path in reverse even through the depths.
I think sometimes they just disappear for a bit. Have you checked for them underground yet? They hang around there sometimes.
To add to this, the dotted line on the map OP has shown is the route in the depths.
Also the lesser dragons, their route is supposed to be 30 minutes. Perhaps just stand at top of tower Thyplo for a bit and look towards east
Wait, does that imply "greater" dragons?
I believe they're referring to the Light Dragon.
Dinraal is consistently the hardest one for me to find as well. I don't think the castle quest blocks the dragons.