RPE Document Builder fails to start after V6.0.6 iFix001 upgrade

We're using WebSphere V8.5.5.13 to host CLM in a distributed environment.  One host has the JTS, GC, LDX and RPE applications. I was able to get RPE V6.0.6 integrated successfully last month and everything worked properly.

Today I updated the CLM tools to V6.0.6 iFix001.  RPE will not start after this upgrade.  I suspect the RPE depends upon in the directories that are deleted from the profile (temp, wstemp, workspace) during the upgrade.

In the trace file, I get messages like this:

org.eclipse.jst.j2ee.commonarchivecore.internal.helpers.WARFileAnnotationsDetector locateAnnotations Failes to create class reader for [ module-info.class ] in [WEB-INF\lib\javax.json-1.1.jar ]; [ null ]
org.eclipse.jst.j2ee.commonarchivecore.internal.helpers.WARFileAnnotationsDetector locateAnnotations Failes to create class reader for [ module-info.class ] in [WEB-INF\lib\javax.json-api-1.1.jar ]; [ null ]
org.eclipse.jst.j2ee.commonarchivecore.internal.helpers.WARFileAnnotationsDetector locateAnnotations Failes to create class reader for [ module-info.class ] in [WEB-INF\lib\javax.json.bind-api-1.0.jar ]; [ null ]
org.eclipse.jst.j2ee.commonarchivecore.internal.helpers.WARFileAnnotationsDetector locateAnnotations Failes to create class reader for [ module-info.class ] in [WEB-INF\lib\javax.yasson-1.0.1.jar ]; [ null ]

Then the rpeng and dgaas applications won't start. I'm thinking that re-deploying the com.ibm.rpe.web.app will resolve the issue. 

Anyone have any other suggestions?

Thanks,
Fran