Here is how you can clean this up and proceed with pledges moving forward:
  1. Under the Configuration tab, click on Installment Recalculation Defaults 
  2. On this page, you can set the overpayment/underpayment default behavior of LCRM 
  3. At the very least, for underpayments, set "Add Installment to the End of the Schedule" as the default, and click Save
This forces LCRM to add an additional installment to the end of the pledge for the outstanding balance of the pledge. You can also choose a setting for overpayments. It allows the system to handle the calculations itself. Once the above has been set:
  1. Create a new pledge 
  2. Generate the schedule and installments 
  3. Manually edit the installments on the new pledge to match the single gift entries from the old pledge 
  4. Once all new installments are set, the single gift entries can be reversed and deleted 
  5. Once the single gift entries have been deleted, the old pledge can be deleted 
  6. The new pledge should now have completed installments, and the pledge should have generated new installments based off the new underpayment settings.