Wrongly taken dual registration

one of our friends have vat registration and migrated the said registration in GST , however, mistakenly a new GST registration have been taken on another PAN No. and all the e-way bills regarding inward and outward supply have been executed on the new GST registration no.
whereas, all the GST liabilities have been discharged on old migrated GST registration.

now the department has raised the query regarding the liabilities on the newly take registration no Under GST.
However, my friend has applied for cancellation of New GST registration.
kindly state, what could be the department
action, whether any recovery may be initiated by the department. kindly elaborate it.