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It is possible to update iBook using Calibre after the 12.7 iTunes update, but it is a real pain. I'll document all the steps in the hope that it will assist whoever's able to update the Apple interface plugin:
To remove existing books from iBooks:
1. In the iBooks app, go to My Books, tap on Select, select each book you wish to remove, then tap on Delete. You can't remove books using iTunes anymore, as far as I can tell.
To add books from Calibre to iBooks (on a PC):
1. Connect your device to your PC with a USB cable, and launch iTunes if it doesn't open automatically. Click on the device button in the top ribbon (the one you'd normally click to pick which books to sync). Books are no longer located under Settings, but will be present under "On My Device"--click it. This should show the list of books in iBooks--click Sync if necessary to synchronize. Note that you can't check or uncheck any of the books from here.
2. From the Edit menu of iTunes, select Preferences and go to the Advanced tab. Note the iTunes Media Folder location.
3. Launch File Explorer and navigate to the directory found in Step 2. There should be a Books subdirectory, and under that will be one folder for each author, with ebook files inside of those folders.
4. Launch Calibre. Instead of Connecting to iTunes (which will no longer show you which books are on your device), Connect to Folder, and pick the Books subdirectory from Step 3. Send ebooks to or delete from your device as usual, and these changes will affect the Books folder from Step 3. Close Calibre when you're done.
5. For each book you want to upload to your device, go to Explorer, go into the folder for the author, and drag the ebook file into iTunes, and on top of the Books icon under "On My Device"--they will then appear in the list, and in iBooks on your device. I tried dragging folders to make things easier, and it didn't work.
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