Save a copy will be greyed out if your file is currently hosted from another computer. If you move a copy of this file to your machine and open it directly with FileMaker Pro, it should then be an option that you can try.
You could also try using Export Field contents to export a copy of the file and then re-inserting it. If that works for you, a script could loop through all your records and perform this same manipulation on all your PDFs.
The Export Field Content command and reinserting it does not work. I will have time tomorrow to move a copy of the file to my machine and work on making a compacted copy.
Thank you for your assistance, it is much appreciated.
While you are at it, you might recover a copy of the file to see if the recovered file has the same problem.
Thank you for your posts.
In case there is some corruption in the PDF file, export the PDF file, open the PDF file in Preview and re-save it. This should write new information to the file. Then, Insert the new PDF file back into the Container field.