I guess my question back would be whether you have changed any of them to "user topics". If you make any change to a topic, such as its name, any of the topic weights, the term or document cutoff, then the topic is changed into a user topic. Then when you generate new multi-term topics, it intentionally eliminates the one that is closest to the topic you have modified: that way you don't have to look at essentially the same topic twice. Does this correspond to what you are seeing?
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