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Your problem is a misconception:
There is no fixed connection between what an annotation rectangle happens to cover and the stuff underneath that rectangle.
An annotation can be defined anywhere: over images, vector graphics and also empty space.
Therefore the annotated text (this is a misleading term - as explained!) does not care or take note of whether it is covered by an annotation.

What you can do is removing the text underneath an annot rectangle by defining a redaction annotation with the original annot.rect and then applying all defined redactions. This will remove desired text.

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@siddhesh-provision
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