Not sure if understand your question correct, but it is not possible for you to map the account and userrole into non-persistant entities instead of the entity directly.
That way, you can process the non-persistant entities anyway you like and there for set the reference set instead of adding.
Inside of the import mapping, instead of doing 'find by key' or 'create', you can do 'retrieve by microflow'.
In that microflow, you can clear the reference set.