If you use the propre sp, things whill work fine.
This is because these procs also tell the running sqlagent to refresh its job-data.
I use it all the time when e.g. I schedule db-maintenance, the first thing I do is disable the incremental backup job plus leaving a notification.
I do it this way :
EXEC MSDB.DBO.sp_update_job @job_name = N'myserverLog_Incremental', @new_name = N'DBMaintenanceProcedure_Disabled - myserverLog_Incremental', @enabled = 0
the last step contains the reactivation of this inclemental backup jop
EXEC MSDB.DBO.sp_update_job @job_name = N'DBMaintenanceProcedure_Disabled - myserverLog_Incremental', @new_name = N'myserverLog_Incremental', @enabled = 1
Works as desinged 
Johan
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