After deleting the process you can manually mark the transactions as not acknowledged in order to re-run the process.

Create a Revenue query to find a list of all transactions marked as acknowledged.
  1. In Analysis select Information Library 
  2. Select add an ad-hoc query
  3. Highlight revenue as the source view and click OK
  4. Under browse for fields in expand revenue letters
  5. Drag Acknowledge date from select revenue letters fields to include records where
  6. In the apply criteria window enter the date you ran the acknowledgements and click OK
  7. Add any other fields you wish to see in the results to results fields to display
  8. From the preview results tab highlight the transaction and select browse
  9. Select revenue transaction page from the choose page definition window and click OK
  10. Complete the steps below to mark the transaction as not acknowledged 
  11. Move to the next transaction in the query results and complete steps 8-10 until all are complete
To remove the acknowledged status
  1. From the revenue transaction page click on the payment hyperlink 
  2. Select the letters tab
  3. Highlight the letter and click delete
  4. Select Yes to the message "Are you sure you want to delete this letter?"