I agree with "Big hammer" and find it easier to just remove the bolt and nut from the shock arm and slide the arm off the shock's shaft, leaving the ball part of the arm still inside the link. It may help to insert a chisel or flat blade screwdriver in the arm's split opening behind the bolt to spread the opening a little bit. Move the rear axle up and down with the floor jack to facilitate an easier arm removal and re-installation. You'll find the "sweet spot" where the arm will be easiest to pull or pry off.
However, if pieces are missing from inside the link as you suspect, now is the perfect time to rebuild the link's guts. This will make the shocks more efficient and also eliminate an irritating knocking noise when the car hits a bump or hole in the road. Missing internal shock link parts will definitely create a rattle that is hard to diagnose with the wheels still in place, especially inside the rear shock links.
By the way, you can't put the shock arm back on incorrectly and still be able to install the bolt. There is a groove in the shock's shaft for that bolt. Any other orientation of the arm over the shaft will not allow the bolt to be inserted through the rear of the shock link arm.
Marshall