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It may be easier to change your Transfer Account, since it is true the system won't let you change opening balances/year end closing accounts.
Generally, a transfer between related companies is a note receivable on one company and a note payable on the other. Try changing the account type of the transfer account to other account type/other current asset or other current liability. (If you use accounts receivable or accounts payable, you will have to enter a customer/vendor name with every transaction). You may need to create a new account for these transactions.
The equity account (usually called retained earnings) used for year end closing should not have anything in it except the automatic year end entry that rolls into the opening balance of the new year.
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