It's not related to syntax editing. It has to do with how deselection of things is handled. While it would be theoretically possible to keep track of every selection made in a rule, and then diligently go through and remove all settings related to the object that was deselected, this would be a huge undertaking affecting hundreds of lines of code. This in turn would directly affect the efficiency of the app, as it has to load every time it runs. And all of this effort for what? The cosmetics of the settings in app settings and In Use By? It is purely cosmetic, and has no impact on how your system works. 'Fixing' it would have a negative impact on how your system works.
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