In the area of biomedical engineering, digital-microfluidic biochips (DMFBs) have received considerable attention, because of their capability of providing an efficient and reliable platform for conducting point-of-care clinical diagnostics. System reliability, in turn, mandates error-recoverability while implementing biochemical assays on-chip for medical applications. Unfortunately, the technology of DMFBs is not yet fully equipped to handle error-recovery from various microfluidic operations involving droplet motion and reaction. Recently, a number of cyber-physical systems have been proposed to provide real-time checking and error-recovery in assays based on the feedback received from a few on-chip checkpoints. However, in order to synthesize robust feedback systems for different types of DMFBs, certain practical issues need to be considered such as co-optimization of checkpoint placement and layout of droplet-routing pathways. For application-specific DMFBs, we propose here an algorithm that minimizes the number of checkpoints and determines their locations to cover every path in a given droplet-routing solution. Next, for general-purpose DMFBs, where the checkpoints are pre-deployed in specific locations, we present a checkpoint-aware routing algorithm such that every droplet-routing path passes through at least one checkpoint to enable error-recovery and to ensure physical routability of all droplets. Our experiments on assay benchmarks show encouraging results in terms of latest-arrival-time and routability of droplets. The proposed methods thus provide convenient reliability-hardening mechanisms for a wide class of cyber-physical DMFBs.