Patching overrides modified module.xml. How to preserve it?

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Issue

If modules from EAP are modified like following files, it will be overrided after patching.

/jboss-eap/jboss-eap-6.2/modules/system/layers/base/org/jboss/as/remoting/main/module.xml
/jboss-eap/jboss-eap-6.2/modules/system/layers/base/org/jboss/as/server/main/module.xml

Is there a way to preserve the files?

Environment

Red Hat JBoss Enterprise Application Platform
- 6.2.x

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