I think it's lovely of you to be so caring and concerned about your friend's sister and to earnestly desire to help her. I think Siralex's advice of treating her as you wish to be treated and to not stop loving her is very wise advice and really the best you can receive.
It's common for a college student's personal and religious beliefs to transform as they transition from their teenage years into adulthood. I haven't even begun college yet, and already in the past year my beliefs have been modified, expanded, and changed as I've been exposed to more thoughts and reconsidered some of my own. Growing up the way people view and interact with the world is frequently influenced by their families and culture, and when they fly from the nest their perspectives change. For some it's a gradual and subtle evolution as they mature, and for others it's more radical and abrupt. To an extent I think it's actually healthy because we all need to examine our beliefs and moral compass for ourselves, determine what we sincerely believe in for our own reasons and not just because it's what our parents or church have taught us to believe, and recalibrate the compass if needed. To me it's part of the "unexamined life is not worth living" maxim where you reflect on your life and how to give it direction, meaning, and purpose. Many who diverge from the pathways of religion they'd grown up taking then return to them after exploring other faiths, beliefs, or simply living and gaining experiences, knowledge, and maturity.
I don't know if you're familiar with Ask.Fm, but my account there sort of became like an unofficial advice column of sorts after I stopped writing an actual advice column for my school newspaper a couple of years ago. I'm guesstimating that around a fifth of the questions I've received have related to religion. A girl just wrote a few nights ago about how she'd been a devout Catholic for 18 years, happily attending parochial schools and Mass, and unquestioningly believing in God and loving him. She's now in the second semester of her freshman year of college, and is home for spring break where her mom is prodding her to attend Mass daily. She's grappling with her faith and has dreadful anxiety about returning home for the whole summer and "coming out" as agnostic. Her ideologies had all been molded by Catholicism, and college exposed her to an expanse of other beliefs that fractured that mold. She's torn between wanting to still participate in the church-related activities she loves and being a part of the community she always belonged to, and feeling like she'd be a hypocrite. She's afraid her family and friends will judge her, or worse reject her. Protestants, Jews, Muslims, and others have written about similar concerns. Many feel vulnerable and defensive. A fractured faith can quickly become a broken one if the wrong force is used. I think that's why it's important to make each person who wants to be there genuinely welcome at church.
I think aggressive attempts to pull a person who believers peg as having strayed from their faith back into the flock can make that person bolt and run in the opposite direction. The very term militant atheist implies defensiveness. Combative people often feel like their beliefs have been attacked (even if they were done so nicely and without malice) and disrespected and so they go on the offense to protect and maintain their position. I think praying for an atheist can be kind, but that telling him or her that he or she is being prayed for could make him or her feel resentful. Some atheists perceive that as passive aggressive and pious, even when it's good intentioned and earnest. Sending links, attempting to persuade the person to return to her faith, and all that is thoughtful benevolence, but could repel her and push her back rather than pull her in. I would simply treat her as her, and encourage your friend to do the same. You don't have to accept beliefs to accept the person who holds them. It's likely that the less resistance her sister encounters with her atheism, the less the urge to militantly defend it will be. It would probably be for the best for your friend and her family and you to focus on everything else going on in her sister's life and everything else that makes her who she is instead of zeroing in on her atheism. I would avoid cajoling, proselytizing, nudging and the like and just let her be. Hopefully her family and friends will be careful to not make her feel like she's being patronized or tiptoed around, but also won't be in her face about Christianity. If her sister hasn't already done so, she might want to ask her why she's an atheist and then really and truly listen. The purpose of that conversation shouldn't be to debate, challenge, or try to talk her back into her former beliefs, but to seek understanding. That in turn could help the two of them to have productive conversations later on about faith, if they willingly choose to have them. Some people who become atheists never revert to their faith, while many others do. I think being like a beacon of light, something that is a constant but mellow and unthreatening source of light, can help to guide someone the most effectively.
