The cleanup steps advice people to do the analogous:

[standalone@localhost:9990 /] deployment-overlay redeploy-affected --name=singleton-deployment
[standalone@localhost:9990 /] deployment-overlay remove --name=singleton-deployment --redeploy-affected
Deployment overlay singleton-deployment does not exist. 

but that will fail, since that deployment overlay is already removed, so it doesn't know which have been affected.

The fix is to run the --redeploy-affected straight on the add/remove commands!

Same issue in the provided CLI scripts.