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The failure after the first "step 6" doesn't surprise me. The import must run to fully put the book into the database. I'm not sure what it does, but I think it sets up a UUID and fills in other tables. When you restart calibre without having run the import, calibre's scan might see "wrong" information and might put that wrong information back into the database.
Speculation: your second set of 5 steps fixes that by resetting the database for the book to what it is when the book is first sent. The import (series 2 step 3) sees the new book and does what it needs to do.
Speculation: the third set fails to match the device because the UUID in the database doesn't match anything in the calibre library. Does using "Match book to library" in the device view fix the problem? Matching the book will update the UUID in the kobo database.
You didn't say whether the "normal" sequence works or not, where "normal" is to skip from section 1 step 4 to section 3 step 1. My guess is that it works, as that is what most people do.
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