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I've been thinking about this issue for some time now, and have mostly come to the same conclusions as you have. I also think EPUB (version 2) is the most future-proof format, having the best chance of still being able to be be read and written many years down the line.
What I do is the following:
- Import books into Calibre, removing DRM in the process.
- Export the book (Save to Disk), and stash the DeDRM-ed original somewhere else.
- If not EPUB: convert/unpack (in case of azw3) to EPUB.
- Use the Calibre tools to remove errors and/or change the book as I see fit.
- Convert the book to AZW3 (as I have a Kindle).
So yes, my main format is EPUB, even if the original book is an AZW3 that would be usable on my Kindle without any changes.
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