We have released an sql-ledger 2.8.24 patch which corrects the following bank reconciliation issues:

1. When there are multiple receipts for a single invoice/date or same
   amount/date, only one is shown. This happens when
   * When source column is blank for both payments
   * When source column contains same value for both payments.
2. Marking one receipt of *same* invoice as reconciled will
   incorrectly mark the other receipt as reconciled as well.
3. Reconciled transactions are displayed on reconciliation screen
   forever making it inconvenient and error prone to do the
   reconciliation.

Patch can be viewed here.