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Buy nowThe Net Income line item on your Balance Sheet should be the same as your P&L Net Income when the P&L and balance sheet are both run with the date range This Fiscal Year-to-date (or when using a different balance sheet date than today, when the P&L date range starts on the first day of the Fiscal Year and ends on the same date as the balance sheet).
This is true when the reports are both run on the same basis, either cash or accrual. And it also should be true even when you get that message about the balance sheet being out of balance (which is Intuit punting because they didn't want to do the work to make the balance sheet balance...)
From your description, it seems like you might be running the P&L for a different date range. Is that possible?