That sounds bad. I had loads of errors listed in the migration logs (just done 4 migrations) but 99% were informational and those that weren't were easily fixable. I'm really unhappy to hear you had such a bad time of it. That's the last thing anybody needs on their plate, especially if a quick fix is not available.
But are we talking about
ERROR: () Execution of /usr/local/psa/admin/plib/api-cli/ipmanage.php -u 126.96.36.199 -ssl_certificate_ref long-string-of-numbers-and-letters -ignore-nonexistent-options failed with return code 1.
Certificate does not exist.
ERROR: (domain object domain.tld) Execution of /usr/local/psa/admin/plib/api-cli/dns.php --set domain.tld -list /usr/local/psa/PMM/tmp/dnsKwAyrJ -ignore-nonexistent-options failed with return code 1.
Unable to restore the DNS zone: an error occurred while adding the webmail.domain.tld IN A 188.8.131.52 record: Such CNAME DNS record already exists.
I had loads of those but they were purely informational in my case and no harm done.
I also had loads of passwords generated, but only for mailnames with no mailboxes/passwords or for the occasional Domain Admins who didn't have a specific password. I've not heard of the password problem you have experienced. I didn't know any Plesk passwords were encrypted in anything other than 11 (apart from the admin password itself) .
I'm obviously looking at the wrong bits of the Parallels forum