ITC on RCM - allowability - Goods and Services Tax - GST

Our client has availed services from Transporter for transportation and paid RCM on same. The client has availed the ITC which was paid in RCM. Later on the transporter has denied for services during GST search proceeding, which was claimed by our client. And due to denial by the transporter the department is denying the ITC and asked to reverse the ITC which was claimed through RCM paid. Whether department can do the same ? Any remedy or argument against stand of GST department ? Thanks in Advance.