Emails that have been archived will often alter the form name or some other variable in the Notes mail file.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]
This is caused by the Archiving product taking possession of the email and stamping it with what ever is necessary to integrate it with Notes. Some leave a doc link behind, some change the form type some make other changes.
Edit the NotesDTApp.ini and in the [Notes] section add the following line:
If there are multiple form names, you can add them all, making sure you use the correct format:
You may also specify one or more form names; the first listed name is the default. To define more than one, use a pipe character ( | ) to separate each pair:
MemoForms=memo|phone message|another name|etc
Running the migration again will migrate those elements that were not migrated previously as they had a unknown form name.