When you perform a JIRA upgrade, it will wipe-out changes you made to files (these files include setenv.sh, server.xml, cacerts, and many others).
If you are using the binary installer, it will detect which files have been modified and display them. If you are using the tar.gz to perform the upgrade, then you'll need to have tracked which files you made changes to yourself.
Once the upgrade is complete, you'll need to put your modifications back in place. There is no way to around this.
For SSL specifically, as Jobin stated, you can use Apache for that and take it out of your JIRA configuration. However, if this is not feasible for you, or if you have other modifications (e.g. JVM memory tunings you've made for your environment) you'll need to put these back.
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