With JBPAPP-9973 fixed I tried this scenario from JBIDE-12643 which should now work:

1. Add EAP 5.2.0.ER4 server
2. Create a dynamic web project (or whatever)
3. Start the server
4. Deploy your project
ASSERT project deployed
5. Remove project
ASSERT project undeployed
6. Go to MBean explorer and stop the deployer
From https://community.jboss.org/wiki/SmokeTestJBToolsServerSupport?prevContainerType=14
12) Open MBean Viewer,
a) note that the server can now be expanded,
b) under it are mbeans. browse down to jboss.deployment -> URL ->DeploymentScanner,
c) double-click DeploymentScanner, go to "Operations" page, click "stop" in viewer, click "stop" button on the right,
d) verify operation completes successfully
7. Repeat steps 4. and 5. - this time nothing will be deployed
8. Start the deployer again - see step 6
9. Repeat steps 4. and 5. - still no deployment - FAIL

But it doesn't work - when you stop the deployment scanner (step 6) and try to deploy your project again, it will get deployed.

I suspect that the publish operation checks if the deployment scanner is active and if it's not it will enable it again. If that's the case then this probably isn't a bug. But then we can no longer use that use case in any testing (i.e. disable deployment scanner and check that nothing can be deployed).