Hello
If you want to split the ABAP and Java part with two separate databases then you need to:
Create a new Java system by exporting and importing the Java stack from the existing system to the new system.
Remove all the J2EE related parameters from the profiles of the ABAP stack (if there are some)
Replug the newly created Java stack to the ABAP stack (UME).
Did I answer your question correctly ?
Regards
RB