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Yes, you are missing something.
If we loaded the AAVSO data at a point in time, it would slowly become out of date. This would then generate errors rather than warnings for those charts during observation uploads. When you provide a chart recognised by the BAA database, it then checks the comparison stars match, their magnitudes, and checks the photometry calculation. So adding data that becomes out of date would cause bigger problems than just accepting a warning message.
The whole point of the charts in the BAA database is to allow checks and recalculations. As the AAVSO use numbered comparison stars based on the magnitude, this means star 102 in a chart at one point in time, can be replaced by a different star later. That would corrupt the calculations giving incorrect results. I would not implement a system that I know would give incorrect results under realistic scenarios.
It is much simpler to accept the explanation that you can ignore the chart warning if you don’t expect the chart to be present, as per the user guide for the database.