Going by my own experience, it's not a glitch if the book is on your memory card and in a format other than sony's own. When you format a book, it only formats in one size. If you change size while reading, the reader has to reformat the whole book again into the new size. While that is happening, you get the 'no entry' signal and just have to patiently wait for it to happen. Turning it on/off etc is just going to cause probs which might be why your collections were affected. Don't know for sure since I've always done the patient waiting thing.
Of course, if I'm wrong, then I've been putting up with a glitch forever LOL
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