JB -- once fish get a sufficient dose of rotenone to kill them, it can't be reversed. So, by the time they come to the top of the water, it is almost always too late to save them. You'll need to do any transfer of fish prior to applying the rotenone.
We used to be allowed to use sodium cyanide to kill fish, and it was a reversible treatment. When the fish came to the top, we'd quickly net them, and put them in fresh water. Often (not 100%), we could revive them. However, we can longer use this chemical, for obvious reasons.
Dave