System Refresh: Abap+Java stack

Have a few questions about CRM refresh I'm working on. Done many refreshes over the years and the new process has me shaking my head in disbelief.
Performed a normal system refresh, by restoring online backup of production system onto mirror system. The mirror system exactly matches my production sytem (Oracle 10g, SuSE Linux 64 bit, UNICODE). 
Now my system is running from Abap stack perspective, however Java components fail to load.
Now from reading the documentation (System Copy for SAP, Based on SAP Netweaver 2004s Abap+Java) it appears that I have to use sapinst and no longer use online database backups for system refreshes.
Is this the case? Has the investment my organization made into online backups now worthless?
Is there a way to take the java schema in this online copied database and bring it online after converting it to work on the mirror landscape?
Or should I throw out our system methodology and start new

Thank you for the reply.
Reading SAP's documentation seems to imply that I need to extract out the java schema from my production source and then re-install on my QA target to make a refresh of the java stack possible.
However, if I have a complete copy of my source system database working on the target, why is the extract necessary?
At least, I should be able to extract out the contents from the source as if it was the target, thereby eliminating any sort of production outages (we have many constraints about shutting down production from fuctional perspective).
I'll do some research around the other tools mentioned to see if they can lend a hand fixing the issue,

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