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I found that Calibre replaces the old with the new automatically.
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This is true. And usually fairly safe as long as the plugin developer doesn't change the internal naming convention of the plugin (either purposely or accidentally). If that happens you will probably end up with two conflicting versions of the plugin that may be hard to track down when debugging.
Even if you remove a plugin that has customized settings... those settings will be retained when the new version is installed (provided the internal naming convention is the same). So there's really no downside to removing the old version first.
While you will likely have no issues with replacing the old with the new... it has no advantage over removing and reinstalling. In fact... removing and reinstalling may save you some headaches in the future.
Or something like that.