I assume you are referring to "linked" PDFs, not those in local Zotero storage (under Zotero\storage - Zotero should always be able to correctly delete "stored" PDFs) ?
Why is the link no longer working ? Is the PDF file no longer at the linked location ? Would you still like to access that PDF ? (ie there should be ways to fix a broken link).
In general, "linked" PDFs that you really do want to delete should be deleted via the delitemwithatt plugin (I believe the Zotmoov plugin now also does that). That is needed because Zotero does not delete a linked attachment file when you delete its parent item (so if you rely on Zotero for item deletions with linked files, you will end up with "orphaned" PDF files that are still on your disk but which Zotero no longer knows about). https://www.zotero.org/support/attaching_files#linked_files But in order for delitemwithatt to work, it must be able to find the linked PDF at the location where Zotero thinks that PDF should be.
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Why is the link no longer working ? Is the PDF file no longer at the linked location ? Would you still like to access that PDF ? (ie there should be ways to fix a broken link).
In general, "linked" PDFs that you really do want to delete should be deleted via the delitemwithatt plugin (I believe the Zotmoov plugin now also does that). That is needed because Zotero does not delete a linked attachment file when you delete its parent item (so if you rely on Zotero for item deletions with linked files, you will end up with "orphaned" PDF files that are still on your disk but which Zotero no longer knows about).
https://www.zotero.org/support/attaching_files#linked_files
But in order for delitemwithatt to work, it must be able to find the linked PDF at the location where Zotero thinks that PDF should be.