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
