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Yes, store the reading status and the annotations using the plugins.
The problem for backing up and restoring the annotations is the reference in the data. Each annotation has a reference to the book as it is described in the database. If the books are put back on the device with exactly the same path and file name, it is easy. But, if that changes, then the reference has to be created properly.
Changing formats is a problem. The internal location reference used for kepubs and epubs is different. There is no easy way to convert between them. This also goes for different versions of the same book in the same format. The location is specific to the version of the book as it uses the internal structure of the book.
And while I'm mention it, the same goes for different devices and reading apps. They all tend to invent their own way of recording the reading position. It's probably possible to convert for devices using the Adobe RMSDK (I'm pretty sure I can between Sony and Kobo), and the conversion from Kobo to the calibre reader (epubs only) is easy, but for most devices it won't be.
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