lies upon lies
OP didn't come off the best in her posts. But, maybe biased by my own experiences, I see a mom who has been blindsided by this. Her daughter, who just recently told and recanted a pretty big lie about her mother beating her, is stating that her brother raped her. I think OP understands that her family life as she knew it is over. Either her son raped her daughter or her daughter made serious false allegations against her son. It sounds like her gut is telling her to believe her son -- the question is why? because she truly feels that it didn't happen? or because her mind is rejecting the horror of what did happen?
OP, my daughter made false allegations against my son. She was a prolific liar and we had her in counseling and she had two psychiatric hospitalizations by that point. I didn't believe her, in her accusation her 2 year old brother raped her when she was 7 and had been raping her since she was 5 (he was a newborn and they didn't live together). I had the benefit of "proof" in that it was impossible that the baby got out of the crib and forced her to do anything. It came to light during continued counseling that she had been raped in her foster home (we adopted her when she was 6). She was scared that the rapist would find her if she told on him so she blamed her brother. She also stated that she picked that brother because she didn't like babies and thought she could get him removed from the house. My daughter has serious mental illnesses. The intensity level of the lying suggests that your daughter needs competent, long term care by mental health professionals -- either to help her deal with being raped or to find out the basis for her lying -- or both.
You haven't mentioned a dad. Is it possible that you had a friend who did this to her? That is the 3rd possibility, that she was raped but is blaming the wrong person because of fear, etc. (DO NOT question her about it, just think who you allowed around your children near the 08-09 school year.)
IMHO you have to walk both sides of the path. When you are with your daughter, you need to support her 100%. With our daughter, even though the allegations were clearly false, we felt that they pointed to a deep fear inside her. We installed keypad locks on the bedroom doors (so she could lock people out NOT for us to lock her in) and an alarm on her door. That way she knew only her and her parents (us) had the code to her room so none of her siblings could get in her room while she was sleeping. The alarm also reassured her that even if someone broke the lock, the alarm would wake her up and bring us running. Definitely look for a good, experience therapist. Your local children's psych hospital might have some good recommendations. If your daughter talks about wanting to be dead, please take her seriously and get her to the ER for a psych eval. Many victims of sexual abuse try suicide. Many pathological liars try to up-the-ante and get more attention with a suicide attempt. Either way, she would need intensive help ASAP if she threatens to hurt herself.
Listen to CPS. Do what you are told. Stay out of the investigation. Accept that you cannot control what happens.