You'll have to check this yourself, but when I add a note to a sideloaded book, that note ends up in Kindle:\Documents\My Clippings.txt
Just a guess; but I think the .mbp files, when it's a side-loaded .mobi, really just keeps track of last page read. not bookmarks or highlights or comments.
But that's if they read and commented on the Kindle. You mention they read in another app; so idk where the comments might be if they used Kindle for <insert other device here>.
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