Have the ROE's been filed with Service Canada? If they have, it is not necessary to process ROE's in Quickbooks. Open the departed employees' profile>Employment info tab and enter a release date and ROE code and mark the employee Inactive.
Regarding the warning - perhaps the YTD Summaries are entered incorrectly. Go to Employees>Payroll Setup>Setup YTD Amounts. Make sure that the correct dates are selected in the second window that pops up (Screenshot 1). If those dates are correct, perhaps the YTD Summary is not completed correctly. Be sure to enter amounts for ALL payroll items assigned to each employee - including both employee and company items (Screenshot 2).