Hi KylieD,
Thank you for your post, however sorry to see no one has responded to your query yet.
I will provide the answer to your query just in case you haven't resolved this yet, and for the benefit of other users in the same situation.
When clearing the 'already paid' contributions through the Pay Liabilities function, you need to select the account that the money had originally come out of, as well as the original date the payment was made. By reversing the batch payment, the transactions will be reversed from the account (almost like it never happened), so the payment would need to be recorded again and posted to the original account through Pay Liabilities.
If you have any further queries, please do reach out.
If my response has answered your enquiry please click "Accept as Solution" to assist other users find this information.