Ok I was able to fix this on my own since support takes years to reply it seems... Basically you have to delete your original kvs file that you created with JVM (JAVA) after creating your new letsencrypt files and then re-run the config.sh..
Whoever programmed this Atlassian software with these dumb port numbers and its own built in webserver without the the ability to simply manage SSL easily needs to be fired. The fact that you have to jump through soo many hoops to just use software and have it run well and secure your own devices is caused by whoever was the architect that and these issues should have all been addressed by now considering the size of Atlassian.
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