I do not believe the embassy will deny your petition and her visa application based on your petition. Before, your wife was trying to come to the US as a non-immigrant while she had I-130 filed for her. Now, she is coming as an immigrant.
Att. number 917-885-2261 This advice does not create an attorney client relationship. No specific legal advice may be offered by the lawyer until a conflicts check is undertaken. Information sent through a web form or via email may not be treated as confidential. Please accept my apologies for spelling mistakes. Law Office of Alena Shautsova www.shautsova.com www.shautsova.com www.russianspeakinglawyerny.com
The sister's visa and student visa do not invalidate your visa. It is not a basis to deny the visa you filed, the fact that her sister also filed or the fact that she was denied when she filed for a student visa.
The above is intended only as general information, and does not constitute legal advice. You must speak with an attorney to discuss your individual case.