Problem with paragraph style overrides and character formatting

I've had this problem for a long time, and sometimes it resolves itself, sometimes it doesn't. Finally I'm begging for help.
I am typesetting academic articles into a journal. We use endnotes. The endnotes have both italic and regular formatting--italics for book and journal titles, and foreign phrases.
Sometimes when I place the text, the formatting reverts to whatever it was in Word. To try to fix that, I've begun stripping the Word formatting from the original document, making everything "Courier New" and just importing it like that. I figured this would clear a lot of the problems I've had with fiddly formatting issues.
I was mistaken.
Here is what happens:
When I place the document it comes up in the original Courier New font, with italics and other formatting intact. If I click "article style" which is the main article paragraph style format, normally it changes. but if I right click and select "apply article style" it is more likely to change the paragraph to the proper style, with italics and other formatting still intact.
But when it gets to endnotes, I'm sort of screwed.
My endnotes style is a bulletted style, so that I can have the endnote numbers consistent. but this seems to screw all the style formatting.
Here is what I do:
With the cursor in endnote text, I click "bulleted endnote style". The character format remains the same, with a + beside the style. The endnote number format is different, however. If I click "clear overrides" it does in fact change to the proper formatting, but it strips any italics or other character in the text. This is frustrating because many of these endnotes have lots of italicized journal and book titles, and it takes a long time to figure out which ones I need to reitalicize manually.
I have tried to use the "customize style import>Style mapping" but it has not fixed anything.
Please help me figure out how to make these transitions more smoothly. I am open to suggestions both on how to make the changes once the document is placed in the Indesign file, and also making modifications to formats in the native Word file so that I don't have these problems.
Thanks
Dan

Sorry, that last message wasn't supposed to send (if that's not obvious!). I was writing it and got interrupted. Damn iphone.
I know why there are two numbers. This is not an issue. What I didn't finish writing was that, the note number before i bullet it is a different font/ format. Again, not a problem. Here is something interesting, though. If I delete that original number by placing the cursor in the middle of it (say a between the 4 and 2 of 42) then delete everything by Shift+arrow forward, press delete then delete the rest of the unnecessary characters, THEN apply the style formatting, it works just fine. Is it something to do with the character codes of those original note numbers?
Word drops in so many hidden codes that it screws everything up!

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