The best thing to do here would likely be to convert those items to relative links, so they’re all contained in the .data folder for the library.
To do so…
1) Highlight your entire list of Records within EndNote
2) Click the References menu
3) Click the “File Attachments” submenu
4) Here, choose “Convert to Relative Links”
This will make a relative linked file for that PDF, instead of using the absolute link to the PDFs external location.
If the links are already broken, you should be able to use Tools - Find Broken Attachment Links, which should create a list of records whose attachments need relinking.