Right now if you change from one scheduler to another while there are running schedules, it can leave running orphaned cron jobs. Add a check for that specific case (using the new scheduler cfield on JobState added in https://dagster.phacility.com/D5919) prompting you to update.
Hopefully someday soon everybody will be on the daemon scheduler and this won't be a problem. Until then, detect this case and raise an error prompting you to go through the migration steps, which are to switch back to the old scheduler and run 'dagster schedule wipe'. The reason we need you to change the config back is that sometimes the wipe command uses the config (looking at you, K8sScheduler).