I have posted an issue about the location of the fields on the github forum and brought this to the developer’s attention, I know this change was very recent and maybe there is something that can be done. I don’t know if there’s a fix for it or not as ACF needs to run on some hook in the comment form in order to work. I’m not familiar with the hooks in the comment form.
As far as querying posts by custom fields on the comments, I don’t know if that’s possible, since they are attached to the comments and not the posts. I think you would need to query the comments and get a list of unique post ID’s and then use a post__in query for the posts.
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