Actually, I do not agree with AndrewB's answer. In my experience, it should work according to your expectations. Using the readernames fields to manage replication has been part of my standard arsenal for 15 years, and I found it much more reliable than the selective replication alternative - it is evil and should be avoided at all costs, but it's a different story!
It is true that once the readernames field no longer contains an entry for server B, the note itself is invisible to server B, but the fact that the note has changed is not invisible to the replicator. The replicator should notice this, determine that the server server no longer has rights to the document and delete it - without leaving a stub.
Have you tried to clear the replication history on both sides?
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