In WAS, stopping server and uninstalling application are important steps to re-deploy.

SET ProfileLoc=C:\IBM\WebSphere\profiles\Machine1-Node1

SET ServerName=Machine1-Node1Server1

SET AppName=apps

call cmd /C %ProfileLoc%\bin\stopServer.bat %ServerName%

call cmd /C %ProfileLoc%\bin\wsadmin.bat -c "AdminApp.uninstall('%AppName%')" -lang jython