CPN Tools does not natively support cloning a substitution transitions, or pages or group containing substitution transitions, with all its subpages. You will only get new instances of the subpage represented by any substitution transition. This can be annoying when editing nets where subpages only differ a little bit.
This is a guide to work around this limitation.
Clone the substitution transitions to another net and back.
To perform a deep cloning first clone a group containing the desired substitution transition to another, possible new, net. Now you can clone them back to the first net and get real clones of the subpages.