The general definition of the hybrid flow shop (HFS) environment is a set of S ≥ 2 production stages where at least one of these stages includes more than one machine, which can process one job at a time. A job can be defined as several operations to be performed by none, one, or more machines at each stage. Usually, these jobs are completed in some sequence between the different production stages, and in the case of setup activities, products are grouped in batches with buffers of work in progress between different production stages. Today, flexible production systems permit in some instances to relax job precedence constrains with alternative process cycles and to group together different batches of similar products in order to reduce setup activity incidence. On the other hand, the availability of multiple parallel machines in a single production stage makes it possible to split the lot size between different resources. This paper aims to solve the HFS scheduling problem in a flexible multistage batch production system, offering a heuristic procedure, to minimize the production makespan and increase the productive capacity utilization using a batch aggregation/splitting strategy while introducing the “workload leveling function” concept. The results are compared with other important scheduling rules widely accepted in the industry and made part of an industrial application. The company used as a test sample is an Italian rotor shaft manufacturer. The final result is illustrated to validate the proposed heuristics.