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Certificates for apps are normally included in the installation package that you execute when installing in the first instance. You cannot restore apps from a backup, which I am guessing is what has happened here, they need to be reinstalled from the original installation file.
It's the third party java certificate stored inside the authority certificate in the phone security settings. They are deleted and i need them for the signing of java applications. Can I still recover them after software upgrade?
You can't recover or restore those certificates before or after firmware upgrade. Best way is, uninstall those Java application from your mobile and reinstall it in your mobile. Only fresh installation can fix this issue.