Emails that have been archived will often alter the form name or some other variable in the Notes mail file. Whilst it might appear that the mail is still in the mail file, it might only be a pointer to the archived email.
In the case where the form has been changed, locate the new form name. This can be found be examining the log file to see what form is being skipped.
The error message will look something like this:
WARNING: [7342-4-7-00000000] Message was filtered or skipped because: Not migrating unknown message form: ARCHIVESTUB [the name of the form might be different]
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