Hi Diferg,
When you process an update event, the pay period amounts are not sent to the ATO so they will appear as $0.00 in the reporting tab. An update event only sends the employees updated year to date amounts. I'd recommend checking the year to date reports for those employees to make sure the year date amounts are correct.
From what you're describing it sounds like you've processed the pays twice which would explain the double up.
As you've entered a negative pay now to clear out the double up, you can do a manual superannuation adjustment to fix extra superannuation. If you're doing this via the browser please make sure to hit the minus button twice to record the negative super amount.