You need to first contact HMRC and ask them to delete the CIS Return of the desired period from their record. 

Once done you may delete the HMRC submitted CIS return by navigating to Bookkeeping>>CIS>>CIS300>>Action Drop down>>click on delete and then you may prepare and submit another CIS return for the same period again and submit it to HMRC. 

We would further recommend you to please download the response of HMRC from the action drop-down before deleting any return.