I understand that this is the case where the goods are returned without issuance of any GST compliant document by the customer. Moreover, the goods are at the transporter's godown instead of the premises of supplier of goods.
Movement from transporter godown: As the customer has refused to perform any movement of the goods, the responsibility of causing GST compliant movement has fallen on the supplier. Considering that the movement of goods is for "reasons other than supply"(as return of goods is neither a sale or a purchase), therefore Delivery challan should be issued by the supplier for movement from the godown to his own premises. E way bill could be issued based on that Delivery challan.
Regarding credit eligibility for the return of goods: A credit note could be issued by you, Section 34 of the CGST Act allows issuance of credit note where the goods are returned by the customer. The supplier can reduce the tax liability to the extent covered in the credit note, provided that the customer has reversed/not availed any credit on the original supply. Hence, it is to be noted that the benefit could be taken, by reduction of tax liability rather than by availment of ITC.
Issuance of goods to other customer from the transporter's godown: Performing supplies from a location not covered in the registration certificate of the supplier is not allowed. However, this hindrance also offers its own solution. If the transporter's godown is added as an additional place of business in the supplier's GST registration, then supplies could be made from that registration. However, it is recommended to clearly indicate the bill from location and the ship from location on the invoice and e way bill.