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Thanks for the investigation and explanation, Sanne.
I was attempting to use a Lucene Filter to limit searched records to a subset of records whose IDs are or are not present in another field of the same index (but different record(s)). After your explanation, I follow the javadoc on org.apache.lucene.search.Filter better, and can understand why this use case wouldn't work out in a filter: the sub-reader filtering the current index segment would only be able to read the values for the referenced field within the current index segment.
Given this, I don't think there's any clarification to be made in the hibernate-search docs, either.