As well as the database, the annotations for epubs on the main memory are also stored in a file. This file is created by the RMSDK and is not deleted when you delete the book. That means that when you put a new copy of the book back on the device and open it, the annotations will be loaded from this file. I believe the lock-ups are caused by the locations the annotations in the file refer to not existing in the new file. When the book is opened to a page the annotation should be on, it hangs.
If you delete the annotations before deleting the book, the annotations will be removed from the file. Or you can delete the file when connected to the PC. The annotations are in "Digital Editions/Annotations". Within that, it matches the path to the book.
There is also a bug related to these files and reopening an epub. When you reopen an epub that has annotations, the chapters that are shown in the annotations list is changed to the current chapter. The annotation still go to the correct place, but the display is wrong. If the epub is on the SD card, the annotations file isn't created and neither of these problems happen.
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