I did the exact same thing you did with 50 rounds of 223. I messed up with the bullet seating die, squishing the shoulder of the cases on a lot of the 50 rounds.
What I did was to use a Frankford Arsenal Bullet Puller to pull the bullets. This in itself was a big pain in the you know what for some of the cases, perhaps because I had crimped the bullets.
http://www.amazon.com/Frankford-Arse...=bullet+puller
Anyway, after pulling the bullets and salvaging the powder I de-primed the cases using my Lee universal decapper. For the first one I was really nervous, I put a towel over the press to catch the blast just in case but all of them de-primed really easily. I have since de-primed other cases with live primers (mainly from crimps not being fully removed, causing the primer to get stuck half-way) and at this point decapping live primers does not concern me very much. Of course I always use eye protection and a light touch but in my experience they extract real easily.
After de-priming the 223 cases I resized them with the full-size die and they were back to spec, no issues. I even re-used the primers and they all fired without any issues whatsoever.
If I was to find myself in the same situation again (hopefully not) I would remove the decapping pin from my full-size die and just do a full resize with the primers in the case.
In short, in my experience with squished shoulders for 223 I had no issue whatsoever resizing them back to spec and I have had no issues removing live primers (I always use eye protection and an easy touch).