I use the reading list plugin with a custom column to do that.
I add books to one reading list to synchronize books to the device, and another reading list to remove them from the device. The first reading list sets the custom column to Y, the second sets it to N and both lists are cleared after synchronizing with the device.
If a book is deleted on the device, there will be a Y in the column, but the book won't be on the device, so it's obvious it was added previously.
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