Cyber-physical systems are hybrid networked cyber and engineered physical elements that record data (e.g. using sensors), analyse them using connected services, influence physical processes and interact with human actors using multi-channel interfaces. Examples of CPS interacting with humans in industrial production environments are the so-called cyber-physical production systems (CPPS), where operators supervise the industrial machines, according to the human-in-the-loop paradigm. In this scenario, research challenges for implementing CPPS resilience, promptly reacting to faults, concern: (i) the complex structure of CPPS, which cannot be addressed as a monolithic system, but as a dynamic ecosystem of single CPS interacting and influencing each other; (ii) the volume, velocity and variety of data (Big Data) on which resilience is based, which call for novel methods and techniques to ensure recovery procedures; (iii) the involvement of human factors in these systems. In this paper, we address the design of resilient cyber-physical production systems (R-CPPS) in digital factories by facing these challenges. Specifically, each component of the R-CPPS is modelled as a smart machine, that is, a cyber-physical system equipped with a set of recovery services, a Sensor Data API used to collect sensor data acquired from the physical side for monitoring the component behaviour, and an operator interface for displaying detected anomalous conditions and notifying necessary recovery actions to on-field operators. A context-based mediator, at shop floor level, is in charge of ensuring resilience by gathering data from the CPPS, selecting the proper recovery actions and invoking corresponding recovery services on the target CPS. Finally, data summarisation and relevance evaluation techniques are used for supporting the identification of anomalous conditions in the presence of high volume and velocity of data collected through the Sensor Data API. The approach is validated in a food industry real case study.