I guess you modified your gameinfo.txt to get ep2 materials working in hammer, every release comes with a new gameinfo, so you have to make a backup of your changes before you update oc or they will be lost.
That only adds day of defeat source content. For ep2 you just put "ep2". Also, check the gameinfo.txt in the obsdk.zip\bin\ep2 as to how the order of the mounts should be. Otherwise you'll be putting CSS or DOD content in your maps that could be taken from regular hl2 or ep2 instead.