Help Desk Ticket Reference: https://c.na7.visual.force.com/apex/Case_View?id=500A000000BdlYp&sfdc.override=1
Steps to Reproduce: Start a default EAP6.0.0 and use the following cli:
/server-group=main2-server-group:add(profile=full, socket-binding-group=full-sockets)
/host=master/server-config=server-two:write-attribute(name=group, value=main2-server-group)
:restart-servers
# replace appone.ear by an available archive
deploy appone.ear --server-groups=main-server-group --name=test.ear --runtime-name=a.ear
deploy appone.ear --server-groups=main2-server-group --name=prod.ear --runtime-name=a.ear

# the next command will remove the content and the domain config become inconsistent
undeploy test.ear --all-relevant-server-groups
Workaround: Workaround Exists
Workaround Description: Don't deploy the same archive with different deployment names.

Use '--keep-content' parameter and check the deployments.
project_key: JBPAPP6

If a deployment in a domain is the same file, deployed with different names to different server-groups, it become the same SHA1.
In that case the stored content will not be updated and the <deployments> section become a new entry which is used by the second server group.

But if one of the deployments will be undeployed or updated the content is complete removed but the second deployment entry is still available.
The second deployment can be used as long as there is a action to it (e.g. restart).

In that case a FATAL error is thrown:
[Host Controller] 11:43:36,493 ERROR [org.jboss.as.controller.management-operation] (Controller Boot Thread) JBAS014613: Operation ("add") failed - address: ([("deployment" => "prod.ear")]) - failure description: "JBAS010876: No deployment content with hash 0807c2c28e5feebb8dfb905788e53b104ecb89fc is available in the deployment content repository for deployment 'prod.ear'. This is a fatal boot error. To correct the problem, either restart with the --admin-only switch set and use the CLI to install the missing content or remove it from the configuration, or remove the deployment from the xml configuraiton file and restart."
[Host Controller] 11:43:36,496 FATAL [org.jboss.as.host.controller] (Controller Boot Thread) JBAS010933: Host Controller boot has failed in an unrecoverable manner; exiting. See previous messages for details.