It could be caused by incorrect folder permissions, so ensure directories are set to 755 and files to 644. Additionally, check the .htaccess file for any rules blocking access to PDFs and, if necessary, add a rule to allow access. Clearing your cache, especially if you're using a caching plugin, may help recognize newly uploaded files. It's also important to review your server configuration to ensure there are no rules or file size limits causing the issue, and confirm that the URL structure for new files matches the older ones.