Did you get a successful outcome for your issue? I ran payroll and am ready to submit my direct deposits but it is saying I have 90 modified checks and 1 voided one. I spoke with Intuit and they said it's a stuck check situation and go ahead and submit it. I ran the audit report and it affects each and every Direct Deposit back to April! What it looks like is that the DD check number is missing in the prior entries and added in on the current one. I double checked a couple of them randomly and they do match what was actually issued. 

I am the only user, so I know for a fact that absolutely nothing was modified let alone 90 payments! I had just run a payroll update and it pulled up this glitch and changed everything. 

Have you gone ahead and submitted your payroll and found that nothing duplicated and everything was fine? I'm hesitant to do so.