ODM will not overwrite files in the target OneDrive that were not migrated from the source. If a user manually downloads files from the source OneDrive and manually uploads them to the target OneDrive, then ODM should ignore these "manually" migrated files as out of scope of the ODM migration process.
If a file was migrated, and updated in the target, then you can use the options in the OneDrive migration wizard to control whether or not the file is overwritten in a subsequent migration.
Note: As always, we would suggest performing a pilot migration on a small scale to validate your particular migration scenario and expectations.
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