"and the bank download feed did not go back that far"
Banking has nothing to do with this entry.
"Normally, I credit the Fixed Asset Accumulated Depreciation account and debit the Depreciation expense account (thereby reducing income on P&L since it is an actual expense)"
It's an Allowance, not an Actual Expense. And All Expense and Income is closed to Equity for prior years. It's always there, seen as Net Income in the current fiscal year and as Retained Earnings, later.
You need to Debit the Fixed Asset account for its cost basis, Credit the Depreciation fixed asset account for the depreciation, and that should be all you need; in the case of something not fully written off as expense, you would credit the difference to Equity.
"to account for this. I don't know how to account for the 2016 depreciation expenses since if I do this it will show a negative bank account balance"
It's Never part of Banking' depreciation is not Real Expense, not an Actual, and no Money was ever involved. That's why it is called Depreciation Allowance. It's a "not real money but Tax value" entry. Never hit Banking, even with current activity, for Depreciation.
