The apps I have experience from allow you to add books from any folder on the tablet, so the same ebook file can be shared by several apps. But I suppose that may be different for different apps? And also how you add the books to the apps.
Typically, if you use calibre, I would expect that you transfer the files to one folder tree on the tablet and use them from there. That is how I do it, only one copy, even if I can read the books using several different apps.
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