You use linked accounts when you have values that can be either debit or credit. The Linked Accounts screen is where you establish the link between the debit account and the credit account. When using AE Reporter, there is a conflict with using Linked Accounts and printing using sub-accounts which can result in the Balance Sheet being out of balance. To eliminate this issue remove all Linked Accounts, leaving only the Bank Accounts.
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Follow the menu path: Reports > Report Setup > Linked Accounts.
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Focus on the relevant Linked Accounts and press D. Repeat for each linked account.
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Close the Linked Accounts window.
Check the Balance Sheet report to confirm the balance sheet is now in balance.