The Adobe-signed situation is a bit more difficult for me to say. My experience with Adobe-signed pdf files is that there is a “Signature Panel” that can be displayed when the file opens in an Adobe software program (in Acrobat Reader, there is a banner across the top that says “Signed and all signatures are valid…” and has a button “Signature Panel”). However, this panel would not be visible if the PDF had been e-signed, then printed, then wet-signed, then scanned.
If pressed to make a recommendation, I would use your eTMF to certify as a copy the final/combo-signed file, and also upload to your eTMF the originally e-signed pdf file (the file with the signature panel) as an attachment, or as an alternative rendition, or as a related document. In this way, you would be preserving the original, partially executed record together with the certified copy of the fully executed record.