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Hello Katie – my understanding is that your CROs are providing you with wet-ink original signed documents, and you want to know how to turn such documents into (electronic) certified copies in your eTMF system. Hopefully your eTMF system already has (or can be setup with) a process for a user to upload a scan of a wet-ink document and attest that the scan is an exact copy of the original, with all of the same attributes and information. In this way, your eTMF audit trail captures the relevant information about this important decision.
As for the documents that are partially wet-signed and partially Adobe-signed, do the Adobe signatures also include some kind of signature certificate file/information? If so I would try to include/attach/relate such files in your eTMF system so that they are always available for review with the record in your eTMF system.