I administer an organization with 7 offices, 6 of which run W2008 and the 7th, the HO runs 2003R2.  Between all of the offices there are several fully meshed replication groups setup to replicate shares.  I am rolling out a new FS at the HO and performing the initial seeding of these replication groups.  I assumed that the new partner would automatically use the local server as it's primary replication partner for the initial seeding, however it is not.  It has many connections open to all of the file servers as well as the local.

Is there a way to force the new 2012R2 FS and DFS rep member to replicate with eh 2003R2 DFS rep member?

Hi,

You could set a DFS member as the primary member in the replication group, it will be considered to be the authoritative member and it wins out during the initial replication. This will overwrite the current replicated folder content on the non-primary member.
 
You could try a command to set another server as primary:
Dfsradmin Membership Set /RGName:<RG Name> /RFName:<RF Name> /MemName:<Member Name> /IsPrimary:True

Note: please do a backup on server 2003R2 incase data is overwritten by the data on server 2012R2.

Regards,

Mandy