Haven't received an official response.  Hope they reset them.

Word is they're trying to reset it all. Fingers crossed.

Siege Mode - Resources Reset

Hey, Raiders! 

Due to a technical glitch in the new Siege game mode, some users ended up having some extra Mana Orbs and Defense Scrolls, which, of course, creates some unfair advantage for their Clans. We already fixed the glitch, and today, we have removed the extra resources gained due to the glitch. Thus, all Clans will start the Battle phase on equal ground in terms of Scrolls, Orbs, and corresponding bonuses.

Please check and update your Clan's defenses and bonuses in case the mentioned resources have been reset in your Clan.

Woohoo!  One for the goodies.