Use a secondary ledger but only for a portion of our primary ledger accounts

We want to use a secondary ledger but only for a portion of our primary ledger accounts. For example, we only want to use it for some of our companies and accounts, not all of our companies and accounts. We have that mapping setup. However, when we run the Transfer Balances to Secondary Ledger scheduled process, it ends in error saying "Target account code combination information to use for the balances transfer is missing." The log then lists all of the account combinations that do not have a mapping, of which are companies we do not