Do the following multiple times:
keytool
-importkeystore
-srckeystore mycompany1.root.ca.jks
-srcalias mycompany1.ca
-destalias mycompany1.ca
-srcstorepass mycompany1.ca
-destkeystore container.root.ca.jks
-deststorepass container.root.ca
-importkeystore
-srckeystore mycompany1.root.ca.jks
-srcalias mycompany1.ca
-destalias mycompany1.ca
-srcstorepass mycompany1.ca
-destkeystore container.root.ca.jks
-deststorepass container.root.ca
The first time you do it the container.root.ca.jks would be created. The subsequent times it will just be filled up with new and new keypairs (public and private keys).