Personally, I would be more worried about the problems with the device needing to be setup again if the battery runs out. Does this happen if you power the device off? If so, the internal micro SD card might be failing. Replacing it might fix this.
And if it is, then it might explain the problem with processing the books on the external card. The database that contains all the details of the books is stored on the internal card. If there are problems writing that database to the disk, it would slow things down and might cause a complete failure.
What firmware version and how many books are on the card and the internal memory? In the last couple of weeks, I have reloaded about 1200 books on the SD card into my Touch. I've actually done this twice after logging out on the device. Each time the books processing took somewhere between 1 and 2 hours. I meant to time it, but I wasn't paying attention to it when I finished.
The only other thing I can think of is if there is a broken book causing problems. Usually this means the processing finished but the books don't get added. But, a hang like did happen with older firmware with bad books.
Actually, another possibility is power. Can you leave the device plugged in to a charger while the books are being processed? This is a CPU and IO intensive process, so the extra power might help.
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