If one's standalone-full.xml configuration contains something like:

<deployments>
<deployment name="MyWebApp.war" runtime-name="MyWebApp.war" enabled="true">
<fs-exploded path="../../SomeDir/MyWebApp.war" relative-to="jboss.home.dir"/>
</deployment>
</deployments>

whether manually inserted (while the server is not running) or installed via the CLI via

/deployment=ServiceCenter.war/:add(runtime-name=ServiceCenter.war,content=[

])

and a deployment scanner like:

<subsystem xmlns="urn:jboss:domain:deployment-scanner:2.0">
<deployment-scanner name="1" path="../../../Applications" relative-to="jboss.server.base.dir" scan-interval="5000" auto-deploy-exploded="true"/>
</subsystem>

a failure by a deployment-scanner to deploy an application (exploded in my case, though I'm not sure this makes a difference) will cause the explicitly listed <deployments> to be removed from the configuration!

This occurs irrespective of the value used for auto-deploy-exploded and to <deployment> elements that had already successfully been deployed and started.