When I sent my collection to my new Sage, I sent in blocks of 2500 books. Mainly since I've edited and error-checked my calibre collection over the years so I have some trust in none of them causing import issues.
For your step 6, I would either trigger an import using NickelMenu or a reboot, again using NickelMenu. Or possibly both. Then I'd go back to calibre to see if any books in that block did not import correctly.
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