This feature is addressed in the Program Parameters Reference file that is available here :
https://support.quest.com/technical-documents/migrator-for-notes-to-exchange/4.15.1/program-parameters-reference-guide/
Below is a summary of the parameters to change in the program settings.
Data Migration Wizard (MNE)
1. On the MNE console click on the upper right menu and choose Global default settings
2. On the [Notes] section add the following parameter :
[Notes]
EncryptedMailOnly=1
The default value for this parameter is usually 0.
3. Save the global settings parameter file and run the migration.
Self Service Desktop Migration (SSDM)
1. Locate NotesDTApp.ini file
2. Add the following parameter under [Notes] section:
[Notes]
EncryptedMailOnly=1
3- Save NotesDTApp.ini file and run SSDM