You might notice some files can be located in more than one folders in the target OneDrive after the migrations.
Duplication will never occur after the first OneDrive migration, it can only if the OneDrive is re-migrated.
During the OneDrive migration we are using Location + Filename to avoid creating duplicates in the target.
When an enduser moves files from one folder to another in the source, and the OneDrive is re-migrated, the files will be re-migrated to the new target location, despite they were previously migrated.
This is by design, we recommend to share this information with the source users, so they are not moving files or doing any re-organization of the source content while the OneDrive migration in On Demand Migration is not finished completely.
