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I had that same question. I asked 2 engineers about it, and they said that as long as the filter was "after" the comparator, then it should be fine. I got clarification that "after" was indeed the situation in the schematic, so I just went with that. I'm going to ask the engineer that's doing the testing to check that out, though. It seems that the presence of an RC filter on the other branch could affect the comparator, but I'm not sure.
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