Is there a difference in the hostname and SID of the system between the source and the target system then the Java stack wont start.
You can read to this article to understand how the instance ID is calculated.
Understanding the Java Instance ID issue
Also read this SAP note 1924336 - Java node 'Instance_bootstrap' terminated with exit code 508
If this is during a DR then I would temporarily rename the hostname of the DR node with the primary one and start SAP (if there is no change in the SID).
Also system copy guides are available on http://service.sap.com/guidefinder
Regards
RB