So the SiteSet class does have a constructor that can accept a vector of IQIndices that could be, say, the sites from two other site sets or a subset of sites from a single site set. So this ought to give you the main ability that you are asking for.
However, when using this constructor one would lose all of the information about local operators that are defined for each site. Is that still something you would need? I.e. to be able to call the .op method for each site after making your new site set?