I think a similar situation happened to me on November 9, 2012. I have a screen shot on my computer, but I don't know how to upload it.
The battle replay is here: http://pokemonshowdown.com/replay/uususpecttest4156102
So this is what happened:
1) The battle between me (dkl65) and ShadowBlast begun. Then, a message popped up: "You have been disconnected, possibly because the server was restarted." The server was not restarted. I pressed "reconnect". So that refreshed the page.
2) I rejoined the battle, but I was in my opponent's perspective. That means the switching Pokemon section showed my opponent's Pokemon. Most of the names are missing. But the movesets are still my Pokemon. When I press a Pokemon icon, it switches into the corresponding Pokemon on my team.
3) As the battle continues, some of my Pokemon faint. That is normal. But when I press some of the icons, it switches in a dead Pokemon (at 0%), and tells me to switch again. So I have to switch until I switch in a live Pokemon.
If my descriptions are not good enough, I can explain it in more detail. I wish that I could upload a screen shot from my computer.