If it will make you feel better you could put a tiny cut into one of the creases on the deflated eggs so that they "can have a good starting point to cut themselves out" lol. It's impossible to tell if your female retained any sperm but even if she did, she would be fine laying again next season. Also there are plenty of late layers this season, I'm sure everything will be just fine. If you are still having trouble get some Melatonin, stuff works wonders.