You can kill one of the machines with fly m destroy and the next fly deploy will respect the machine count.
If you need to scale down to 0 and then scale up, run fly deploy --ha=false , that will launch only one machine if there aren’t any.
At last, we recommend to run 2 machines but enable autostart/autostop to reduce costs while keeping availability.
See Automatically starting/stopping Apps v2 instances and Setting a minimum number of instances to keep running when using auto start/stop