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I feel your pain. I've had to delete Stanza so I can upgrade to OS 3.0. Apparently, Stanza stores epubs in their component formats so one title can easily have anywhere from 20~200 small files. I've accumulated more than 500 books (maybe in a 6-month period? mostly fanfiction) on my iPhone. Some of them, I don't have copies of on my computer since they were downloaded directly from online catalogs. It was already 24 hours since I initiated the back-up and it was only half-way done. Since not having a cellphone for emergency use just so it can finish updating firmware is unacceptable, I took screen caps of all the ebook titles on my iPhone so I can re-download them and then deleted Stanza. The back-up and firmware update process took less than 20 minutes after that.
Mind you, it was mostly my fault since I never backed-up my iPhone. I guess I never really paid much attention before since I didn't have any data of worth on my cellphone. Now that this happened, I'm thinking of a method so I don't have to rely on Apple's back-up process. Unfortunately, even if it's easy to get your apps back, ebook libraries on apps such as Stanza is a major pain in the neck to rebuild. I still haven't gotten to re-downloading all those ebooks.
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