Ok I took a deep dive here to figure out the root cause of the problem:
Previously, Discourse would only pull down emojis that are available across all the emojis sets that we support. However, the addition of win10 emoji set introduced a bug where emojis that are not yet available in the win10 emoji set would cause the emoji to break when we run the emoji update script. After digging through the code, it was clear to me that we need a better pattern here so that we can support all emojis that are in each emoji set.