The issue is that you can only file an amended tax return for the last three years, so you really can not enter all the transactions in the company B accounting file.
I would find the balance of the Due to/from account in company A.
Create a Due to/from asset account in company B
Do a journal entry in company B, if the balance in company A is positive (debit balance), then in company B debit Opening Balance Equity (OBE) and credit the Due to/from account. Then company B pays company A and uses that Due to/from account as the expense (reason) for the payment. Company A deposits the payment and uses the Due to/from account as the source account for the deposit.
If the balance in the Due to/from account in company A is negative (credit balance) reverse the entries in the above paragraph
