If you enter leave directly into a transaction in MicrOpay, there won't be a corresponding leave application in ESS. The leave balance in ESS comes from the Employee's record in MicrOpay and will reflect (be reduced by) the leave taken once the pay has been completed.
If the employee enters the same leave into ESS after you have processed it directly in MicrOpay, the leave application will appear in Leave Processing. It will be included in Not Yet Paid leave in ESS, affecting the employee's leave balance. You will need to import the leave in MicrOpay and then delete it from the transaction, as it has already been paid.
Go to Payroll, Transactions, Import and Export, Leave Processing.
Process the leave.
After completing Leave Processing, go to Payroll, Transactions, Processing, Extended Timesheet.
Enter the Employee.
Select the incorrect Leave from Pay Summary.
Delete the entry imported from ESS.
Make any other required changes, e.g. change the Normal Hours.
Click Process.