General Ledger uses the employee's current Pay Frequency when filtering data. That is, it uses the Pay Frequency the employee is currently attached to and not what they were paid under. If you change an employee's Frequency, then they may be missing from the General Ledger.
To include the Employee in the General Ledger batch:
Go to General Ledger Integration, Transactions, Batch Process.
Select the previous and current Pay Frequency.
Enter the Period End Dates for the transactions.
Enter all other parameters as per your normal selection.
Click Process to extract the data.
Note: You may need to run the Period End Dates individually or in smaller batches to ensure you don't extract periods that aren't required.