It's about time, too.
I hate overtext but love irony.
I've been reading the rules and I noticed that is doesn't actually say that if the overlord deck runs out and you need to draw a card, you shuffle it back in.
I didn't see anything saying that you don't shuffle it either.
Left at that, I would default to not shuffling. That being said, and not knowing how long the typical game is, I would be slightly leery of trimming cards out of the overlord deck in the campaign.
Can anyone let me know if there is something I am missing in the rules?
Yes, you're missing the rule about re-shuffling the Overlord deck:
(p. 16, "Overlord Cards", final paragraph):
The overlord player has no hand limit for Overlord cards. When the
overlord player draws the last card from his deck, he simply shuffles the
discard pile to create a new deck.