You gotta update your CoolReader to latest version (dated May, 24) and apply this instead of what you did before.
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2. Kobo Aura H2O. Fixed "out of border" issue. To apply the fix you should put margin_top=N (N measured in pixels) parameter into cr3/cr3.ini (NOT cr3/data/cr3.ini!). With that full refresh parameter is respected by CR.
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