Also happened to me.
Got through Will and Koga with my Cyndaquil team, took a break, came back to Bruno with my squad of 85's and kept them for the rest of the E4.
Kind of erased the challenge.
However, I had replaced a member of my team with Rotom, then got my guy (A-Raichu) back prior to this fight.
After beating Lance, A-Raichu was replaced with Rotom entirely. I have two of them now.