Was the checkbox for "Store only a Reference" checked? If the GetAsText shows "imagemac" or "imagewin" in front of the file name then its by reference.
Did you upload to the server using the file upload or did you copy the files to the Databases folder? If you copied it manually and the files are stored externally they'll be in the wrong folder (if the container folder was uploaded at all).
These are embedded pdf's (Store only a Reference is not checked). The FM database was uploaded using the File/Sharing/Upload to Filemaker Server... command. I think this may have to do with the default pdf engine although I don't know what that is or how to set it within FileMaker. Currently, pdf's open with Preview (my preferred pdf viewer). I previously used Acrobat, but have tried to remove it from all my machines. Debris issue?