Help: Why does Calibre 5.1.2 duplicate Kindle Scribe 3 entries when adding PDFs?

So I've been syncing my Kindle Scribe 3 with Calibre 5.1.2 for the past month, and every time I add a new PDF—especially those converted from PDF/A—Calibre creates a duplicate entry for the same title. The duplicate shows the same ISBN but a different "Series" tag, and the original entry loses its footnote links.

I have a library of over 12,000 titles, including a 1947 first edition of "The Great Gatsby" I just acquired from a private auction. The duplication is messing up my smart collections and making the library look chaotic.

I've tried the following:

• Updated Calibre to the latest 5.1.2 build.
• Checked the "Add books" settings: "Check for existing books" is enabled.
• Removed the "Series" metadata from the duplicate and re‑synced.
• Disabled the "Download metadata" option temporarily.

None of these steps stopped the duplication. Does anyone know a workaround or a setting I might have missed? Or is this a known bug with the Kindle Scribe 3 integration?

Any pointers would be appreciated.