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You cannot "optimise" the cases in a job list file as it is not designed for that purpose. Optimisation is for an algorithm to search in a large design space by selecting which cases to test based on the "patterns" it has seen in the previous cases. A job list file contains hand-selected cases, which means the user already knows which cases to test. In this case, you just run the whole job list.
I can imagine a scenario where you want to limit the cases in which the algorithm should search within the overall search space. This can be done using the subdomain field in the variable definitions in jEPlus+EA. Or if you need to consider only combinations of certain parameter values, define them first as a combinatorial parameter in the jEPlus project before creating the optimisation project.