Server certificates added to /etc/pki/java/cacerts are removed after running update-ca-trust or system updates in RHEL

Issue

Certificates manually added to the /etc/pki/java/cacerts file using keytool disappear after running the update-ca-trust command or applying system updates (e.g., dnf update).

The user attempted to persist the certificates by placing the PEM file in /etc/pki/ca-trust/source/anchors/ and running update-ca-trust extract. While the Root and Intermediate CA certificates were successfully added to the system truststore, the Server certificate was not imported.