If you gave Dawnstar to the Imperials that may explain why the Pale camp disappeared, because then they don't need to invade it.
The truce is supposed to be in effect until after you defeat Alduin so they can start fighting again without threat of dragons,
so that may be why you can't continue the civil war.
Which means yes, you probably have to finish the Main Quest if you finished Season Unending with a peace treaty.
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And after you defeat Alduin, but Regaining the Pale maybe you will encounter that still doesn't have any quest objectives.
Just go back to Tullius and talk to him, he will give you new orders and you can proceed with the quest.