Hi,
Finally got the solution after a long R&D
What we did just change the module level of application to 2.4 and placed wsdl folder under WebContent.
The main issue was due to annotation processing of the application at the time of deployment.
The deployment process for the module metadata requires a new step to scan the
Java annotations data
from classes that are packaged in the module.
As we are using JAX-WS as a client of WebServices it includes annotation processing. The processing of annotation of JAX-WS requires reading of wsdl files to generate update clients for each deployments. In this process of reading wsdl it was facing problem as its located in WEB-INF folder initially. I just change the location of wsdl and its working fine now.