1. Firstly move an application in the said court for deciding the case after closing her defence , and if rejected, then approach the High court to quash the FIR .
2. Legally, she is not your wife , and without getting the divorce from first wife , the second marriage is not valid
- Further, no rape case made out for consensual relationship / sex
3. Your mother can file a compliant under the provision of Domestic Violence Act against her for the said harassment.
4. Since, she is not appearing before the said case , then follow the reply No.1
5. Legally she cannot get ownership of that flat on any ground , but if she is living in relationship with you for longer period then she can claim residential right from you.
You can contact me, if further suggestion needed.