I don't think DB meant to have people repin locks by removing the bible cover. Illusion's
guide explains how it's usually done. While working with plug followers and tweezers is more of a hassle, it's necessary on some locks.
I had to remove the cover on one of my cylinders once, and it didn't fit as tightly afterward. (I was lazy and didn't take out the driver and spring when I removed a few pins, you can figure out what happened.) I used a little superglue on the sides of the cover, which holds it in place. Another option I've seen mentioned is to replace the cover with small machine screws.