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Ok, well if the JKS file is generated using your current Let's Encrypt certificate files then it should be ok. Currently though, your webserver is serving a self signed certificate (one that you or the software made up), if you think this JKS file is correct and was generated using the Let's Encrypt PEM files etc then make sure you have restarted Tomcat to use the latest version of the file.
Why do you need to analyse the JKS file- didn't you create it yourself? If not then that's your problem!
Your JKS file is a container (a key store) containing the private key generated during the certificate creation and the public certificate itself. If you are using this file then you need to create/update it from the latest certificate information. If you don't know how this file came to be then that's the part you need to look at - either replace it with an updated file or switch to just using the pem files as per the example configs above.