You can delete a counter from the "Counters" menu, by clicking on the trash symbol next to the counter you wish to delete.
It's not possible to delete a counter that is currently in use on a checklist. If a counter is on a checklist's step, you will not be able to delete it. It will be necessary to edit the checklist and delete the step with the counter, and make sure that it has not been attached to a tasks.
Please note that the deletion of a counter is final.