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The various Kobo's do tend to be sensitive to unplugging from USB without being properly ejected, so you're likely right that that is the cause of your problem. If memory serves to do a factory reset on the mini: hold the power button ON for 15-20 seconds (that makes sure the device is off), then press and hold the pin hole in the back and while holding it turn the device ON. That should get you into factory reset which hopefully will straighten out your issues. With luck you shouldn't need to play with the internal SD card etc.
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