I have the same issue and also spent the best part of a day with QBO agents on the phone. One of the agents was able to at least help with part of the problem; that of fixing it automatically so problem goes away.
The QBO agent had me verify/update the bank account number in TWO places under Payroll settings. It appears there are two places in payroll settings where the bank account # should be updated, there is the obviously visible one in payroll settings but there was another, more obscure, location which should have also been updated and the QBO agent had me update this field as well to the correct bank account number. Unfortunately, I cannot recall the navigation to where this second update was made but I know it's there (agents I dealt with were Shadoe S, Alex and Heather, not sure which one fixed it).
I am still trying to find the fix for the second question, that of how to fix the past transactions to ensure an accurate P&L. I am currently having our 3rd party accountant suggest a solution (still waiting for that answer).
