Tested the issue in two different scenarios listed below :

Scenario 1:

When a web-service test EAR(having an EJB JAR/WAR inside it) is deployed in JBoss EAP, it creates a wsdl folder inside the data directory with the name of the deployed application. Suppose, there is an application TestEar.ear having an EJB web-service jar(MyEjb1.jar) in it. When this application is deployed in JBoss EAP, its wsdl will be published at `/data/wsdl/TestEar.ear/MyEjb1.jar/HelloService.wsdl`.

 wsdl
    └── TestEar.ear
            └── MyEjb1.jar
                  └── HelloWebServiceBeanService.wsdl

When the server is stopped or the application is undeployed, the wsdl content is removed from the location, however the folder is never deleted, thereby leaving an empty folder in the "/data/wsdl" directory:

wsdl
    └── TestEar.ear

This is not the scenario when a war/jar application is deployed, in which case the content is completely removed along with the folder.

Scenario 2:

In case of a war, the wsdl folder inside the application has the below structure :

[sanaik@sanaik WEB-INF]$ tree
.
├── classes
.....
└── wsdl
    ├── base
    │   └── as
    │       └── ServerInfoService_schema1.xsd
    ├── ServerInfoService.wsdl
    └── ServerInfoService.wsdl~
...

Deploying the application creates the below structure under "/data/wsdl" directory :

[sanaik@sanaik WsdlXsdExample.war]$ tree
.
├── base
│   └── as
│       └── ServerInfoService_schema1.xsd
└── ServerInfoService.wsdl

On disabling the application via admin console, "ServerInfoService.wsdl" is cleared, however the below contents still remains :

[sanaik@sanaik WsdlXsdExample.war]$ tree
.
└── base
    └── as
        └── ServerInfoService_schema1.xsd

And JBoss does gives the below WARN message :

[Server:server-one] 11:53:30,835 WARN  [org.jboss.ws.cxf.deployment] (MSC service thread 1-4) JBWS024097: Could not delete wsdl file /NotBackedUp/NEW/Cases/CASE-01604047/jboss-eap-6.4/domain/servers/server-one/data/wsdl/WsdlXsdExample.war/base
[Server:server-one] 11:53:30,836 WARN  [org.jboss.ws.cxf.deployment] (MSC service thread 1-4) JBWS024100: Could not delete wsdl directory /NotBackedUp/NEW/Cases/CASE-01604047/jboss-eap-6.4/domain/servers/server-one/data/wsdl/WsdlXsdExample.war

This is only the case if any xsd is placed inside a folder under the "/wsdl" directory and referenced in the wsdl.