Do ask the consultant to show the the updates in the MyCIC account. Or apply for GCMS notes (to get the case history - you don't need the consultant for this, you can do it yourself).
IRCC will most probably not accept your mom's passport after her file was closed. She will probably have to reapply from scratch. In the end, this refusal was clearly avoidable.
On the positive side: A decision on the new application could be made much sooner