Groups are defined by the site profile name, if a group becomes empty then there are no profiles to define it and it will eventually disappear when the tree is re-loaded or the site manager is re-opened.
We've considered addressing this limitation several times in the past but we consider it to be a low priority issue since the impact of this limitation is very minor and non-critical. It is on our TO-DO list but we just haven't gotten around to addressing it.
In addition, most likely we'll need to change the internal and external format/structure we use to store site profiles to resolve this limitation.
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