Those annotations appear to have been fetched from the device using the Annotations plugin. If so, the plugin has some configuration for the styles used. These are applied when the annotations are fetched or updated. But, changing the configuration does not affect annotations already in the library. You should be able to change the colour of the bar, but, will not be able to change the bar to automatically alternate colours.
You can manually edit the styles of existing annotations using the metadata editor, but, that will change the formatting and may cause problems when you fetch the annotations for the book again.
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