Man that happened to me once too so I know how you feel. I lost about five pokemon I had really worked hard to train when I did it. Rest assured since then I've always been extremely cautious when trying that glitch out of fear for loosing any more of my favorite pokes.
I'd say it serves you right for trying to abuse a glitch, but that would be rather...chicken of me.
Just train your team at Victory Road (for Swampert/Aggron/Blaziken/Gardy) and the Sky Pillar for the other two. The experience rates there are quite impressive considering how crap the 3rd gen is for wild pokemon massacre sites, alongside your Emerald Nav runs.