Copy 1 and Copy 3 will always be retained, Copy 2 is only used to move the data from the remote site (seeded data) then no longer required (highlighted below in steps from the doc link you posted).
Seeding process works as follows:
- At Remote Office site, data is first backed up to primary copy.
- Data is copied to secondary copy through an auxiliary copy operation on the USB disk.
- USB disk is physically shipped over to the Data Center site.
- Data is then copied from secondary copy (that is from USB disk) to tertiary copy through Auxiliary Copy operation at the Data Center (or DR site) thereby preventing baseline data transfer over the WAN.
- After copy of data to the tertiary copy, the source-side DDB is manually copied from destination MediaAgent to source MediaAgent.
- Once the baseline is established, secondary copy is no longer required and is deleted. The source for tertiary copy will be modified to primary copy.