To deactivate a program, you can go to Classes > Programs and then click into the program you are looking to deactivate:
From there, you can click Actions > Deactivate:
You may get an error message that "### athletes have this program listed as their default program":
If you get this error, you need to go to People > Athletes > and then select ALL Athletes:
You will then need to filter the athlete list by the Program you are looking to deactivate:
You can then select all of these Active/Inactive Athletes and then change their default to a program that you are not going to deactivate:
You should then be able to deactivate this program as long as you do not have any recurring classes or future WODS associated with this program.