You will need to update the Donation Designation Relationship (DDR) table for the donations and change it from the ID of Southeast Iowa Affiliate designation to the new designation's ID. You can do this with a data loader:

No LCRM Multicenter installed:
  1. Populate the data loader with the donations in question
  2. Change the designation ID to match the new designation ID that the donation will be moved to
  3. Once the records are updated, you can delete the designation
LCRM Multicenter installed:
  1. Populate the data loader with the donations in question
  2. Update the center and campaign on the donations
  3. Change the designation ID to match the new designation ID that the donation will be moved to
  4. Once the records are updated, you can delete the designation