@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!
coadyduffney
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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.