@AKMin I was able to get my application working correctly by changing my packaging method over to jpackage. I was previously using javapackager which seems like it was not bundling the application correctly and executing it via a shell script - the 'universalJavaApplicationStub'. Using jpackage I bundle the app as an app-image, sign all the files, then create a .dmg from the app-image and sign and notarize that and all is working now. Hope this helps!

Currently dealing with the same issue, very frustrating. Did not change anything in my java app, just upgraded to MacOS Sequoia and now it doesn't launch. However I did find a workaround which is to right click the app, show package contents, and find the executable inside the /MacOS folder and run that - app launches fine. I've tried re-packaging, re-signing and notarizing everything but to no success.