The Document Number field is not set to the proper value during a Vault migration using Vault Loader.
The Document Name Format field within the affected Document Type configuration is set to Use Custom Format. This switches the Document Number to a system-generated Document Number instead of allowing for the custom Document Number value to be set during a migration.
The solution is to switch this value to the Use File Name value shown in the screenshot below for all affected Document Types.
- Vault Help Documentation: Vault Help