Because the code uses taxonomy_index, term references on unpublished nodes are not replaced
1. create 2 or more taxonomy terms
2. create an unpublished node with a reference to one of the terms
3. replace the term
The term reference on the node should be updated with a reference to the selected term
The term reference is not updated (although the deleted term is no longer referenced)
tbc
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It's likely this issue predates Contrib.social: some issue and comment data are missing.
I can see where someone might not want an unpublished or draft node to be updated. Perhaps there should be a user option on the Replace page for the user to indicate if unpublished nodes should be included/excluded from the replace.