It's easy to see if the non-Kindle file is in an older format; open it in a text editor like "NotePad"; it'll look like garbage but in the first few characters of the file you'll see an 8-character text string. If this says "TEXtREAD", the file is the older format which doesn't support nav links, etc; if it says "BOOKMOBI" the file is in the modern format.
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