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I posted about this earlier, but want to count myself in the group that is experiencing this problem with large libraries. My suspicion is that the fact that there seem to be fewer problems on the iPhone compared with the iPad is that (I'm guessing) most of us with large libraries don't carry nearly as many books on our iPhones as we do on our iPads. I'm able to sync with no problem with my iPhone using calibre 2.1.0, but the plug-in crashes instantly (with a database corruption error message) as soon as I try to sync with the much larger Marvin collection on my iPad. There are no such problems with calibre 1.48 using the old plug-ins.
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