A JIRA upgrade will flat-out replace a bunch of files that you have customized. They recommend that you re-apply your customization to the new files instead of trying to port your new files forward. It's rather messy, the worst part being the OKTA integration which is kinda nasty.
Add the reverse proxy fun to the port 8080 connector stanza
proxyName="jira.mdr.defpoint.com" proxyPort="443" scheme="https" secure="true"/>
okta-jira-3.1.3.jar
to /opt/atlassian/jira/atlassian-jira/WEB-INF/lib
okta_login.jsp
to /opt/atlassian/jira/atlassian-jira
okta-config-jira.xml
to /opt/atlassian/jira/conf
Okta explains it better than I can. There's some web.xml filter setting that need to be in place.