Sorry,
found the answer myself:
"The users must be stored in the database thats what the configuration in the config tool shows. Alternatively if you want to keep userstore independant of your SAP DB you can use the UME to repoint to other stores such as an LDAP. I assume that an upgrade might not remove the registered users ,but I have seen how refreshing R/3 databases from other R/3 instances brings users from other instances,I am not sure if you can even refresh J2EE databases from other J2EE databases." by Pran
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