Is there any way to edit the save file to make those encounters re-appear?Not unless he changed it. She spawns in the center of the map in Marston avenue. I think she doesn't show up until after day 30 now though. She used to be there on day 1. There is an ambush encounter that I suspect you're talking about which has 3 or 4 females and I think 1 male in the group. So that one you can only capture 1 of the females as well as the 1 male.
I'm many dozens of hours in on a very old save when either it wasn't possible (or I didn't know it was possible) to capture girls from regular encounters, and just defeated them all in fights I believe some capture-opportunities were added to encounters I already cleared as well. It would be amazing if I could bring them back!