Solution

Remove the following entries from the target domain.xml (after the upgrade) and restart the server:

<jvm-options>-Djavax.net.ssl.keyStore=${com.sun.aas.instanceRoot}
/config/keystore.jks</jvm-options>-
<jvm-options>Djavax.net.ssl.trustStore=${com.sun.aas.instanceRoot}
/config/cacerts.jks</jvm-options>