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In the past few years two research groups of Politecnico di Milano, whose activities were centered on Formal Methods for the production of critical software and on industrial manufacturing systems, respectively, have carried out a joint research project that, among other things, aimed at introducing the use of formal methods in the design and analysis phases of industrial production systems (and especially of so-called Flexible Manufacturing Systems, FMSs) as a complementary tool to the ones used in the current practice of the field. This paper reports on the challenges that the research groups faced during the project, and on the lessons that have been learned in the process.