How to upgrade only certain CLM applications on IBM I correctly?

Hello, I open this question for our Customer:
A PMR is already opened for this problem.

Customer is using CLM 3.0.1 on IBM I and upgrading to 4.0.1.
They only want to upgrade JTS and CCM as they do not use QM and RM.

The Info Center upgrade guide suggests to run
upgrade/was_upgrade.sh profileName serverName nodeName wasVersion wasOption maxHeapSize adminId adminPwd jvmVersion jazzAppName jtsAppName clmHelpAppName qmAppName rmAppName adminAppName

However, Customer did not specify all appName parameters, but only those he wanted to upgrade:

upgrade/was_upgrade.sh WAS3RTCP WAS3RTCP S069B765_ WAS3RTCP V7 Express 9045 xxuserxx xxpassxx std64 ccm.war jts.war clmHelp.war admin.war

It seemed OK, as CCM and QM are working fine.

However, Customer cannot login to WAS adminstrative console, seeing
error SRVE0260E:

Excepción de página de errores
SRVE0260E: The server cannot use the error page specified for your
application to handle the Original Exception printed below.

Excepción original:
Mensaje de error: javax.servlet.ServletException: SRVE0207E: Uncaught
initialization exception created by servlet

Código de error: 500
Servlet de destino: /logon.jsp
Pila de errores:
java.lang.AbstractMethodError:
javax/servlet/jsp/JspFactory.getJspApplicationContext(Ljavax/servlet/Ser
vletContext;)Ljavax/servlet/jsp/JspApplicationContext;
     at _ibmjsp._logon._jspInit(_logon.java:123)
[...]

Also, in the JTS/Admin diagnostics he sees:
Error 403: There is no REST service handler registered for the path
"/rootservices" and the same for "/scr"
This is for RM application.

See screenshots:




My question is how to properly use the was_upgrade.sh if we do not want to upgrade all applications?
Also, what are the recovery steps from this situation? The info center states that a backup is being created when was_upgrade.sh is ran.