They have shown several benefits resulting from the deuteration at the 5 prime position by comparing 3422 with the undeuterated version in their examples. In patent terminology these benefits were unexpected and surprising.
(what if) ACHN's production lots contain 1%, 0.1%, or 0.01% of non-deuterated material
The ACHN patent application covers levels of deuterium enrichment at the claimed positions (5-prime of ribose and uridine) of 50-99% in various embodiments. Hence the point you brought up is not a concern if the patent is allowed ... which I expect it will be, based on the four separate benefits of deuteration that are shown in the examples.
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