The Job Estimates Audit report reflect net changes, not new amounts. So if you reduce the Current Estimated Amount of an estimate by $1000, then you correctly will see an amount of -$1000 on the Estimates Audit report.

The same would be the case if you increased the Current Estimated Dollars - the amount that prints on the report would be the net increase.

As you are using Change Orders to reduce the Contract Price for the customer, and editing the Estimate to reduce the Cost, I believe you are doing everything correctly.