As digital microfluidic biochips (DMFBs) make the transition to the marketplace for commercial exploitation, security and intellectual property (IP) protection are emerging as important design considerations. Recent studies have shown that DMFBs are vulnerable to reverse engineering aimed at stealing biomolecular protocols (IP theft). The IP piracy of proprietary protocols may lead to significant losses for pharmaceutical and biotech companies. The micro-electrode-dot-array (MEDA) is a next-generation DMFB platform that supports real-time sensing of droplets and has the added advantage of important security protections. However, real-time sensing offers opportunities to an attacker to steal the biochemical IP. We show that the daisychaining of microelectrodes and the use of one-time-programmability in MEDA biochips provides effective bitstream scrambling of biochemical protocols. To examine the strength of this solution, we develop a SAT attack that can unscramble the bitstreams through repeated observations of bioassays executed on the MEDA platform. Based on insights gained from the SAT attack, we propose an advanced defense against IP theft. Simulation results using real-life biomolecular protocols confirm that while the SAT attack is effective for simple instances, our advanced defense can thwart it for realistic MEDA biochips and real-life protocols.