Sometimes custom workouts are disappearing out of the workout list before they are run. We are working hard to fix this issue. In the meantime if you experience this behavior you can just log out of your Runkeeper account on your phone and log back in. Your workouts will return so you can run them all!
If you would like us to inform you the moment this issue is fixed and an update is released, just click on the "Submit a request" button below and submit a report using the subject line, "Custom Workouts Disappear Before Being Run" with a description of the problem!