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KOReader isn't "gone". An update doesn't touch user content.
Check the jailbreak FAQ for more details, but you'll basically just have to reinstall whatever you require to actually launch KOReader (meaning MKK if you were using KUAL, or kpvbooklet if you were using that).
On a sidenote, I don't know where you got the "DISABLED_OTA" thing from, but that's a new one to me, so I'm not terribly surprised it didn't do a thing besides clutter your USB root.
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