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Mostly "adding to" or "changing" a copywritten publication (ePub) is a big no-no.
Besides the legal aspects, most reading apps don't want to spend the extra time, and/or overhead, to develop the functionality to store annotations in a linked document.
Having said that, there ARE some apps that allow annotations...you just need to track down which ones do it the way you want. (For example: Marvin on iOS, spent a lot of time making annotations possible)
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