The "Not Queued: Migration history is pending update" migration status will appear when the NM server does not receive all updates from the migration worker.
To correct this issue manually without upgrading to current release of Notes Migrator, wait until all migrations are completed.
Restart the NM Worker (where the processednoteid.txt file is located). This should update and send the file back to the controller. Then update the 'updatestatus' column appropriately.
If this doesn't work then:
Open SQL for 3.8 and newer. Open the cmt_uninversal.mdb for CMTe 3.7. and older version.
Go to the 'MigratedMessageTable'
Check the value of the 'UpdateStatus' column. If the value is "Pending". then clear out the value
Close the access db (if applicable)
Restart IIS and try it again.
If this still fails, and all the data was not migrated, then remove migrated data for the user.
Clear the User Migration History
Start the migration again.