To elaborate on problems with deletes/formats (weird if you have to format more than once). Sony's software is caching UI files. It does NOT support working with files that get deleted / changed, for obvious reason. So when you start ebookapps, then change its files in internal memory, you get cache that is half broken as well as file system that is half broken.
So if ebookapps has started, you have NO clean way to modify its files! On the bright side, it doesn't start if you connect it to USB while reader is booting. So as a rule of thumb, when modifying something related to it:
a) restart the reader (settings => advanced settings => shutdown, then switch it on)
b) immediately connect it to USB while it's still booting
c) now you can change files on Internal Memory
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