You guys made the choice to get pregnant knowing she would be alone in Canada given that you PR application would unlikely to be approved at that point. There are women who are alone in Canada with a baby. Your application should be refused because your wife spent all this time out of Canada. Also assume she has informed CRA that she is out of Canada so they can determine if she is entitled to CCB. You will have to see what happens with the application. If refused you will have to apply again.