Answer
There's no direct 'reset the navigator tree' action, but depending on how many configurations are involved, two approaches can achieve something close to it. For just a few unwanted configurations, simply Unpublish them in the Global context — the downside is that any future configuration-and-publish cycle in that context will re-publish the unwanted ones alongside the new ones, since unpublishing doesn't delete them. For a more thorough reset, Unpublish everything in the Global context (which effectively returns behavior to core/unconfigured), create a new Custom context on top of that clean baseline, redo only the configurations you actually want in that Custom context and publish it, then assign that context to the relevant users/company via Configuration Context Mappings (Solution Manager > Configuration > Configuration Context Mappings) and clear the Mapping cache afterward. The tradeoff with the thorough approach is having to redo wanted configurations from scratch in the new context and reassign it to every affected user — but it avoids ever re-publishing the specific unwanted legacy configurations again.