You can save your library as a compressed file (go to the Endnote toolbar and select File >Compressed Library) then move the compressed file to a different location before uninstalling then reinstalling the software.
However, did you first check if moving the PDF import folder to a different location before starting up Endnote allows the program to run but just generate an error message about not finding the folder? If so, check at that point if you can turn off the automatic PDF importing function by going to the Endnote toolbar and selecting > Edit >Preferences >PDF Handling and uncheck the box labeled “Enable automatic PDF importing”. Then click the OK button. You can then move the PDF import folder back to its original location or create a new folder but now when you launch Endnote it won’t automatically try to import PDFs.