When you explain a bank transaction, you can alter the explanation amount (which by default is set to the full amount of the transaction).
If you enter a lower amount to allocate to one invoice for example, once that explanation has been created, some part of the original transaction will still be unexplained. You can then explain that remaining amount against another invoice payment.

You can even mix debit and credit explanations against a single transaction (for example a mixture of invoices and credit notes).
It's fine to have multiple entries explaining a single transaction like this - the only important thing is that the transaction is fully explained.
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