Failed to repair. Lesson learned
I started from the sd card image from David. Here is what I did.
1. Used USB Image Tool 1.72 to back up my device's original microSD card content into an img file (old).
2. Used Hex Editor Neo to open the img file, go to 0x200, and record the serial number (s/n) of my device.
3. Unzipped the zip file from David into an img file (new). The img file is about 4GB, the same size as my microSD drive
4. Used Hex Editor Neo to change the s/n number of into my device's s/n and save the file.
5. Used USB Image Tool to restore the new img file to my microSD card.
6. Put the microSD card back into the device and power it.
It seemed worked. The 4 LED's at the bottom flashed, seems it is booting. Unfortunately my screen got broken during dissemble (blame the waterproof glue).
I guess my initial guess is correct that the file system in the microSD card crashed. However, I need to be a lot more careful in dissembling this. There is a thin glass-based substrate layer which is very fragile.
Having had it for a little more than two years, I am not very satisfy with this device. My main two disappointments are:
1. It missed goto page/location functionality. A lot of times I read a book of more than 10,000 pages and I read the book from different devices. When I need to switch the device, the slide bar is not sufficient for me to go to a specific page. I go back/forth many times to get close, and then touch screen to the right place. My Kindle can specify a page, I can use binary search algorithm to reach a page quickly [log(n)].
2. Sometimes the device is not that responsive. Sometimes it is the touchscreen, sometimes it is the software of the system. When I read a big book (epub), a touch for turn to next page ended with going back multiple pages.
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