Why are modules not updated after applying patch for EAP 6.2.0?

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Issue

Using the following command to apply patch why the modules are not updated. The original jars get corrupted.

patch apply /path/to/zip

Does patching overwrite any of the existing configuration files?

Environment

Red Hat JBoss Enterprise Application Platform (EAP)
- 6.2.x
- 6.3.x
- 6.4.x

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