You're probably using the html file (only) to convert to a Kindle book. The html file knows nothing about the ncx or the opf file. If you have the opf file and the ncx file coded correctly, you need to use kindlegen/Previewer to convert the opf file--which will know where to find the html, the ncx and any other resource files (provided the paths provided in the opf are valid).
The other option is to create a valid epub and convert/upload that.
If you're just uploading files to KDP--and not doing the conversion on your own computer--I don't know the process well enough to assist.
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