It could be that your sister is worried that if your mum gets into a serious relationship, she will see it as a new life and her children will no longer be a priority/even be a hindrance to the 'fresh start'. I'm in no way saying your mum will do that, but unfortunately some parents do and the children can worry about that. Where's your father out of interest? Some background on that could lend a perspective.
Also what was your sister's behavior like around this man? Try talking to her. Although I don't want to jump straight onto it being down to abuse, that is also certainly a possibility. Signs that he was abusive include her being very disengaged around him, avoiding eye contact, perhaps being skittish or hiding in her room, as well of course being terrified of the possibility that he will come back.
Description of how she used to act will also help - has she been generally prone to upset and worry in the past, or more relaxed? Has she responded better to your mum's previous boyfriends if there have been any?