When performing General administrative functions with Migrator for Notes to Exchange (MNE) the Domino Person Document for the user's account is changed to No for "Allow external Directory Synchronization."
The MNE console is by default using the following setting :
DisableNotesForeignDirSync=1
Make sure that the ini settings for your migration and/or the template being used have the following parameter:
DisableNotesForeignDirSync=0
This will allow the setting to remain YES, alllowing foreign domain synchronization.
Note: This can also be set in the UI of MNE.

https://support.quest.com/technical-documents/migrator-for-notes-to-exchange/4.16/program-parameters-reference-guide/11#TOPIC-1264542