Yes, you can do Save to Disk in bulk - just select all the books.
Removing formats - again, select all your books, right-click (or its Linux equivalent - I use Windows) on the Remove icon and choose Remove all formats from selected books.
Adding the files back to their respective book entries - this can be done in several ways.
1. Dragging/dropping the file to the Book Details window, or
2. Going into Edit Metadata and adding the file to the formats box.
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