I would be asking myself why I'm using Kindle platform for this, given its limitations with personal documents.
Assuming this is for something akin to 'long-form' reading, I'd be more inclined to go with something like Google Books or Bookari. Both have 'full citizen' status for ePub and PDF that you store in their respective clouds, with full syncing of reading position and notes. Both have iOS and Android apps and support for desktop browsers.
iBooks might be an option if you are only using Apple devices.
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