Hello Justin,
How did you update your cron configuration? One can redeploy the whole application, or only the cron configuration, for Java, with:
./appengine-java-sdk/bin/appcfg.sh -A your-app-id -V app-version update_cron [YOUR_APP_DIR]
For details and other languages, you may read the "Scheduling Tasks With Cron for Java" documentation
page.
Usually, any change to the cron messages requires that you re-deploy the App Engine application. To avoid this, you could rewrite the App Engine application to pull the YAML file from a Cloud Storage bucket, have it monitor the file for changes, and update App Engine Cron Service when it detects modifications to the YAML file. More details are available on the "Reliable Task Scheduling on Google Compute Engine"
page.