You can clear out due to/due from accounts with a Bank Transfer from the Legal Entity of one Location to the Legal Entity of another. 'Due To' and 'Due From' entries will be created automatically on the distribution of intercompany transactions when the Location in the header of a transaction belongs to a different Legal Entity than the Location in the detail rows. Click here to learn more about intercompany transactions.
Running a Trial Balance, Balance Sheet, or GL Account Detail report on those accounts will show the totals owed at any point in time. From these reports, you will find a 'Due To' amount which can be zeroed out by entering a Bank Transfer for that amount to the necessary Legal Entity. Click here to learn about creating Bank Transfers.