How do I deal with invoices created in a Company file but then customers have paid into the old sole trader bank account?

Hi sandra19, 

You have the option of recording a transfer from the Sole Trader bank account to the correct account and then matching/recording the payment to the invoice.

The process will depend on whether the Sole Trader account is in the QuickBooks Online Company Chart of Accounts or not. 

The steps to complete a transfer between accounts are outlined here: https://quickbooks.intuit.com/learn-support/en-au/banking/transfer-funds-between-accounts/00/263093

Please feel free to reach back out if you have any other questions. 

Rebecca