Hi @Stream_biofilm,
There's not an easy way to do this at the moment. This post details how you would filter your table to some samples of interest (in your case certain replicates), and pull out a "feature metadata" from the summarize visualization, then you can use that to filter against the other replicates and look at the feature counts.
It will be kind of arduous, but you can probably use that to perform whatever "set" operations you need between your replicates.
Sorry there isn't a better way 
If you are more inclined to programming (or know someone who is), you could also load these artifacts using the Artifact API, then viewing them as biom.Table objects make this kind of custom work much easier.