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Exclusively sideloaded ePub. Like you, my annotations are primarily for highlighting formatting or OCR errors (I often scan books and convert them myself), so they get removed when I get the chance to correct the errors.
Are you asking specifically the speed of the highlight long press, or page turning and whatnot? I don't see any significant slowdown in page turning. The difference in long-pressing seem to vary even within a single page - there doesn't seem to be a specific pattern at all, which is strange.
I've gone into the database with an SQL viewer and cleaned out the annotations "removed" from the device but not from the database. I don't recall that specifically helping. But I can give it another try.
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