Hello Cain,
I’m sorry for the trouble you’re having with EndNote’s PDF indexing.
EndNote creates a unique folder to ensure that PDFs do not get overwritten by other PDFs.
And, unique folders containing the filenames is the route we’ve chosen to ensure this doesn’t happen.
In the EndNote Preferences, under PDF Handling, it is possible to adjust the convention by which EndNote automatically renames the relatively linked version of that file.
Otherwise, the best way to get a copy of the PDF attached to an EndNote reference is to highlight the record in the list, and under References - File Attachments, there is an option for “Save As…”, which will create a copy of the PDF attached to that record, and offer you the option to save it wherever you like.
Please let us know in the Suggestions forum if there is something you would like changed, or you think would be an improvement to the software. We’re always looking for ways to make things better.
Thanks!
Steve