Hi
you say you have the reports that were sent to the ATO for the missing pays
are the pays recorded in the employee cards?
have you checked the general ledger to see if they are there
If you do have to recreate the transactions in myob I suggest that you print out the sent ato reports for the missing pays and do journals for them
of course if the pays aren't recorded on the employee card then you may have to redo pay runs .
Ther probably is a way to do that and not report but I would be concerned about totals being skewed..
as far as the accruing of leave , check how your entitlements have been set up the answer is there and check that the entitlements have been included in the employee card also
hope that helps
Lisa