Digital twinning is gaining popularity in domains outside of traditional engineered systems, including cyber-physical systems (CPS) with biological modalities, or cyber-biophysical systems (CBPS) in short. While digital twinning has well-established practices in CPS settings, it raises special challenges in the context of CBPS. In this paper, we identify such challenges and lessons learned through an industry case of a digital twin for CBPS in controlled environment agriculture.