When you have a CT600 loss in the current year, this can be carried back to previous years. An amended return must be submitted for the previous year, or a letter written and sent to the HMRC to confirm the carry back of the losses.
To show the carry back, on the current year return you need to go to Tools / CT / Losses and enter the amount as being carried back and also cross the box on the main form to say there is a repayment due for an earlier period. On the year in which you are carrying back the loss you need to amend the CT600 and file this amended return online.