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I can't answer you main question, but.
I really don't use annotations (clippings.txt) I tried to note book errors to fix them, but nobodies editor has a Kindle-style GoTo location (Dev Hint: a editor Plugin would be welcome for use with the mainstream reader app notes)
Calibre can STORE ancillary files (as you did). That is IT. Nothing else is done.
In your case, You would need to restore the 'file family' to a compatible device (assuming a K allows that via USB) to see them in context
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