If the PDFs are store in your database using FM External Storage you should not attempt to access them other than within FM, and the way to do that is either: (1) set you database up so that you can easily view them within FM (e.g. a full sized version of your Container field or a Web Viewer), or (2) set up a script that exports the PDF and opens it in its native software—Acrobat or whatever. Any attempt to directly access the folders which FM creates to manage External storage will end badly, so just don't do it.
It is possible the folder you are referring to, however, is a folder you created, in which you stored the PDFs that you inserted into your database. If that is so, and you have actually used External storage, then these files are irrelevant as far as your database is concerned.
To add a few more details, a commonly used method is to use Export Field Contents to export the file--usually to the local computer's temporary folder to avoid an unnecessary "file clutter"
a $Variable can be set to the local computer's desktop path like this:
Set Variable [$Path ; value: Get ( DesktopPath ) ]
You can use GetContainerAttributes to get the file's file name or you can use export field contents to name the exported copy differently.
Where this get's sticky is when you want to open the file in the computer's default application for the specified file type, edit the file and then "save" those changes back to the copy stored via FileMaker in that external location. That would require saving the changes to the temporary copy, closing the file and then using Insert File to insert the temporary copy back into the container field.
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If you can open it without FM, it is not secure.