Libra Colour Device metadata stuck after 3nd reconnect

[orchidreader]

Apologies if the title is a bit vague but I've been having an issue with my KLC where after I factory reset, on my third connection with Calibre it no longer sees any new reading progress. Here's a step-by-step timeline of what's happening:

1. I factory reset my kobo. Log in to my account. Pressed the sync.
2. First connection to Calibre: I send my books to Kobo in kepub format. Disconnect Kobo using the Safely remove USB device in the Windows taskbar
3. Wait for the books to finish importing, open a book (let's call it book1) and advance the reading progess to 20%
4. Reconnect the book to Calibre so that the series data gets captured. Calibre will capture the 20% progress of book1 and run the Goodreads plugin. I disconnected my kobo.
5. I open another book (book2) and advance the reading progress to 50%.
6. Third connection to Calibre captures the reading progress for both books (20% and 50% respectively).
7. I disconnect my kobo and open another random book, book3. Change the reading progress to 40%.
8. Reconnect my kobo and it only captures the reading progress of book1 and book2. It doesn't see that book3 has an update to the reading progress. Disconnect my kobo again.
9. Update the reading progress of book1 to 30%. Marked book2 as Unread and progressed book3 to 80%.
10. Connect to Calibre and it sees the following reading progress for each book: book1 is 20%, book2 is 50%, and doesn't see book3.

I've been stuck with this issue ever since I got my Kobo Libra. I have a Kobo Clara 2e that doesn't have this issue. It seems like the metadata for the Kobo gets stuck around the third connection to Calibre. I also noticed that after my third connection, when I import new books to Calibre, after I disconnect and reconnect, the new books don't have the check mark on the On Device column in Calibre even though I can read them in my kobo with no issues.