If your guest leaves earlier you need to shorten their stay in the "Properties" tab of the reservation.
You need to:
1. Open the reservation go to "Properties".
2. Change the departure date to today's date.
3. If you want to apply cancellation fees, leave the box "Apply cancellation fees" ticked. If not, untick the box.
4. Once you have shortened the booking to today, you can check the reservation out as usual.
Note: if you choose to "apply cancellation fees" the system will calculate this automatically based on the settings done in the Rate Group.
If you had already closed the bill of the guest, shortening the booking will automatically post rebates on the guest bill in line with the cancellation policy applied.
Note 2: if you are shortening a booking made by an OTA (Booking.com/Expedia, etc), don't forget to also inform the OTA about the shortened booking, otherwise you will end up paying commission for these nights.