"It appears it is adding deposits twice"
You may not want to revert everything.
If the bank downloaded deposits twice, what you could do is go to the Banking tab > 'Categorized' section > 'All Dates' and filter one month at a time. And click the "Received" (Deposit) column. This will show duplicate deposits for the same amount. It would be easier to Undo duplicate deposits and exclude them from the Banking tab. And the RECONCILE the bank account each month. Hope this helps!