If the repair process is not certified at the OEM, it means that the original manufacturer has to have control over that process. It is usually carried out that the original manufacturer prepares the necessary documents for repair and necessary forms that will be proof that some repair has been conducted and give those documents to the OEM. In a Quality agreement between manufacturer and OEM, this should be stated together with the description of the control that the manufacturer will perform over the OEM repair process. One way to control the repair process is to conduct an audit at the OEM, so-called supplier audit.
Information on performing a supplier audit according to ISO 13485, you can find in the following link: