This doesn't sound like a problem with large books. And the only problems I have seen with large books is performance, and an occasional sickel reboot. And in recent firmware, the latter seems to be only for large kepubs. Both of these problems happen when opening books and reading them.
The problem that can affect paging in the lists is generating the cover images. For everything except kepubs, this is created by rendering the first page of the book. Apart from some slowness, I haven't seen any issues with this except in the firmware versions when sickel was first introduced. This was 3.17 or thereabouts and I'm pretty sure it was only large PDFs that triggered it.
If it is related to the cover image generation, it would be worse with the SD card. For books in the main memory, the images are stored. For books on the SD card, they are not. They are cached in memory for a while, but need to be renegerated when needed. That means it's likely that the problem will keep happening whenever you reach a certain page with books on the SD card, but, for the main memory, it will only need to generate covers that weren't the last time you got to that page. A workaround for this is using calibre to generate and send the covers to the device. It can do this for books on both the main memory and SD card. And if they exist on the card, the device will use them.
If this has been consistently happening for two years, then I'd suspect a hardware problem. The only thing you can change is the internal SD card. For the H2O, changing it means breaking the waterproofing.
Before doing that, the things I would try a factory reset and only putting a small number of epubs on the device to start with. I would convert all the MOBI to epub. I doubt this is a problem, but the overall handling of epub is much better than MOBI, so it will eliminate a variable. Same goes for PDF, at least for a while. They should be OK, but, except for PDF sized for a small page, I just don't find them a pleasant experience. Then try generating the cover images using calibre. You can do this when sending the books, or later using my Kobo Utilities plugin.
If none of that helps, it's time to open the device.
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