Will there be a problem if my new IELTS score is less than the IELTS score at which I got the provincial nomination?You need to contact the province and get your nomination moved to your new EE profile.
IELTS must be valid at the time you submit your complete application. It cannot be expired. So your rejection makes sense and there's no way to reverse that. You have to create a new profile and wait to get ITA again.