I had the same problem.
Log into your Humble Store account, and at the bottom of your "My Library" page you should have a list of "unredeemed keys". Pillars of Eternity + preorder content should be there even though you already redeemed it. Redeem it again, and now you'll have the preorder DLC next time you log into Steam.
I assume Humble messed up giving out the preorder bonuses in the first while where the game was available.