The Silver Fabric upgrade process does not maintain any changes to the Engine JRE which can be problematic if there is an updated Engine JRE that is newer than the JRE that is included in the upgraded version of Silver Fabric.  

When upgrading Silver Fabric, the JRE must be updated in the Silver Fabric upgrade if the custom JRE was already higher than the updated JRE that is included in the Silver Fabric install.

If there is a custom JRE installed when upgrading Silver Fabric, you will need to compare the version of the JRE that is included in the upgraded version with the version of the custom JRE.  

If the custom JRE is newer than the JRE that is included with the Silver Fabric upgrade and you wish to keep the custom JRE, you will need to copy the JRE from the old installation directory to the new installation directory due to the fact that the JRE is not copied over by default during the Silver Fabric upgrade process. 

This process will require a broker restart which is why it is recommended to run this during the upgrade process to minimize downtime. 

You will need to copy and replace the following files from the original installation to the updated installation: 
SF_HOME/webapps/livecluster/public_html/register/install/jre/jre.platform.ZIP 
SF_HOME/webapps/livecluster/public_html/register/install/jre/jre.platform.dat