MNSP is not designed to migrate and maintain the email folder structure when migrating email. The result will be a flat list in SharePoint without the email folder structure intact. MNSP can be configured to migrate folder by folder, but this requires manual effort for each folder.
This scenario is better handled by using a two part migration process with Migrator for Notes to Exchange (MNE) to migrate the Notes email to PST, then a third-party product to migrate the PST into SharePoint.
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