If you have your NNID linked and enter the eshop then all of your pirated DLC will be removed. Back up your emunand, link your NNID and use Decrypt 9 (or w/e it's called) to get your ticket.db, back that up and use FunkyCIA2 to download your eshop stuff as cias on the PC. Then you can restore your emunand and install your eshop stuff as cias.