I don't know what the case law is if Merck finds traces of an undeuterated compound they own in ACHN's product. In the case of crystal morphs, my understanding is that anything detectable represents an infringement, but I'm far from an expert.
"Therefore, if a patent claim covers a crystalline form per se, the presence of that crystalline form at any level - even trace levels - in the API entering the U.S. could subject a party to infringement liability. The quantitation of damages is still a problem without an answer. As no case law on which to make predictions is available yet, different scenarios are possible, following two different approaches. In one case, damages due in the case of infringing would be proportional to the amount of the patented polymorph. This means that if a polymorph were present in trace amounts, the damages due would be negligible (and precise quantitation would be a big issue!). A different approach would be that if even a single crystal of a patented polymorph were present, the damages due would be proportional to the full loss of revenue. This means that the damages would be calculated assuming the whole product were present in the patented crystal form, even if only traces of it were found. In this scenario, the lower and lower detection limits of modern analysis methods become a key factor."