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There is no workflow I know of that puts end notes in a table. Do you mean they're in a text frame (or frames) of their own, placed at the end of the document? That's exactly as it should be in InDesign.
That you got an otherwise flawless import is an event worth celebrating, by the way. End notes in general are a problematic feature, with the problems multiplied by trying to import them from Word.
You could select all of the end notes and paste them into the main flow of your book, after the last content or index or other page, but this will break all the numbering and links. Unless there is some other problem caused by this structure, leave it as is, with the end notes in their own (series of) text frames.
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Title of your post says ENDnotes - but then you are referring to FOOTnotes - can you clarify?
Can you also post a screenshot?
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(Missed that.) Yes, end and foot notes are two separate systems, in Word and InDesign and pretty much every other "word" app. Each is managed by its own menu, settings, and feature set. Solutions for one will not apply very closely to the other, so clarity is essential here.
To the good, it may be as simple as changing the document settings for the note type to get the result you expected.
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