RE: The HG/SS Question and Answers thread
According to Smogon, you can knock out the runners then beat the E4 and they should be back
Steadfast said:PMJ: The ones you can't rematch are Entei, Raikou, Latias and Latios I believe. If you defeat Suicune it goes back to the burned tower and you battle him there. Also I think the other people are correct with Lugia and Ho-Oh in that you rematch them. The ones I'm not sure about though are the birds. I just save before each battle anyways just in case.
Does anyone know if the birds are rematchable?
According to Smogon, you can knock out the runners then beat the E4 and they should be back