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The KoboTouch driver updates the database in three ways. The two main ways are for the collections and to setting the series information. Both are done during the "Send metadata to device" stage of the connection. This is also run after books are sent to the device. The collections will be done for books just sent, but the series info has to wait for the next connection as the database doesn't contain records for the new books. If you have changed any series info on books already on the device, they will be updated at this point.
The other change is if you resend book already on the device and in the database. When you do this, the file size stored in the database is update to match the copy being sent. If this isn't done, the firmware will remove the book from the database and then process it as a new book.
None of this should cause a database corruption. About the only thing I can think of would be if the eject was done to quickly before the database was completely written to the device. Safely ejecting the device should prevent that.
The device will process all new books on the main memory and SD card when it is disconnected from the PC. It will also process all books on the SD card when insert it. So, ejecting and reinserting it should get any books on the card that are not in the inserted database processed.
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