Why are some JARs unusable after applying a patch in JBoss EAP 6

Issue

• When trying to compile against a JAR that was updated with a CP, getting a ZipException java.util.zip.ZipException: error in opening zip file.
• The command: jar tvf $JBOSS_HOME/modules/system/layers/base/org/jboss/xnio/main/xnio-api-3.0.7.GA-redhat-1.jar is not working after applying the patch to EAP 6.2.0. Error is as follows :

java.util.zip.ZipException: error in opening zip file
  at java.util.zip.ZipFile.open(Native Method)
  at java.util.zip.ZipFile.<init>(ZipFile.java:215)
  at java.util.zip.ZipFile.<init>(ZipFile.java:145)
  at java.util.zip.ZipFile.<init>(ZipFile.java:116)
  at sun.tools.jar.Main.list(Main.java:1004)
  at sun.tools.jar.Main.run(Main.java:245)
  at sun.tools.jar.Main.main(Main.java:1177)

• After upgrading to EAP 6.3.2 and configuring logmanager in boot classpath as follows:

-Xbootclasspath/p:/home/jboss/jboss-eap6/jboss-eap-6.3/modules/system/layers/base/org/jboss/logmanager/main/jboss-logmanager-1.5.2.Final-redhat-1.jar 

• We started getting the following ERROR in opening logmanager jar file:

Error occurred during initialization of VM
java/lang/ClassNotFoundException: error in opening JAR file /home/user/jboss-eap-6.3/modules/system/layers/base/org/jboss/logmanager/main/jboss-logmanager-1.5.2.Final-redhat-1.jar

• Why do some of our JBoss jar files appear to be corrupted after applying a patch?
• According to kbase article, JDK 1.8 support is included in EAP 6.3.3. Can we safely use the publicly available JBoss EAP downloads (https://www.jboss.org/products/eap/download/) such as 6.3.0 GA to compile a Java 8 application, even though Java 8 support was not included until the 6.3.3 patch?
• What is the recommend way to get JDK 1.8 support without the corrupted jar problem?
• There is a JAR file in the modules which we cannot open. Is the file corrupt?
• Our Developers found out, that serverall JAR-Files located under modules/ or bundles/ directory in jboss-eap-6.3 are defect after appling Patches. Any advice / solutions?
• We tried to update the unpacked EAP 6.4 with the EAP 6.4.2 on Windows. Afterwards we did a diff using a tool. So it shows up that "bundles/system/layers/base/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.5.0.Final-redhat-21.jar" could not be opened.
  Examining the EAP 6.4.2 ZIP we found this file to be part of EAP 6.4.1 while in the EAP 6.4.2 there is "jboss-as-osgi-configadmin-7.5.2.Final-redhat-2.jar" which could be opened .
• Do you have any idea why
  1) The file is corrut after update?
  2) The file is not the most recent version?

• why are the jars corrupt afterapplying the patches and should we expect this in future patches. Even though at compilation time the read error is logged, it is not the case at runtime. At runtime the jars a readable. Why is that?

• We use -Xbootclasspath to put jboss-logmanager on the boot classpath for the Wily java agent. After applying the current cumulative patch we are getting this class not found exception:

Error Message:  java/lang/ClassNotFoundException: error in opening JAR file /opt/jboss/jboss-eap-6.4/modules/system/layers/base/org/jboss/logmanager/main/jboss-logmanager-1.5.4.Final-redhat-1.jar