As I said in the other thread, I don't think this is related to the beta.
The first thing to do is to check that CC's database is consistent with the book files. Run CC's "Books with missing files" from the main menu. Fix any problems.
Next, connect to calibre. Assuming that the "problem" book is still there (one that shows 2 when only one is in CC), in calibre's library view delete the book. You will see a dialog asking if you want to delete from the device, from the library, or both. Pick device. You will now see a dialog showing the two books on the device. The 6th column contains the paths of the books on the device. These must be different. Note these paths. Now, on the device, use a file manager to verify that these paths point at actual books.
If there are actual books there then the book really does exist twice in CC. If one of the paths doesn't exist then we begin to focus on the problem. In this case, please do the following:
- Connect CC to calibre.
- Delete a problematic book from the device using calibre's delete function, not CC's delete function.
- Disconnect CC.
- Restart calibre in debug mode.
- Reconnect CC.
- Verify that the book is not on-device. If it is then stop here, sending me the calibre and CC debug logs.
- If the book is not on-device then send that one book to CC. The book should now show on-device, 1 copy. If it does not, stop here and send me the CC and calibre debug logs.
- Disconnect and reconnect CC.
- If the book now shows more than one copy on the device, send me the CC and calibre debug logs.