Get your taxes done using TurboTax

You to fix the errors as you did or TT wont let you file.  You won’t be audited with zero errors in your return.  The brokerage companies should have fixed their files to follow the IRS new rules of no negative numbers. The end result after the fix is still a loss and your tax return refund/payment does not change, so no way can I imagine an audit being flagged.