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I mess with updating metadata heavily using kobo/calibre.
The only way I've ever corrupted the database was by accidentally unplugging when the device wasn't properly ejected, or resetting the device when it hung.
The kobo utils have not corrupted the database on me. However, as some operations *do* require ejecting and letting the kobo scan the files, it's real easy to accidentally unplug without ejecting while doing that.
As to deleting/re-adding a book to update metadata, the only metadata that this is actually required for is:
* filename on device (who cares about this anyway?)
* table of contents within the book
* other formatting changes within the book
Some metadata like shelves and covers can be added when the book is added.
Most other metadata has to be added after the book is scanned by the device. using the calibre kobo utilities plugin.
I think covers are cached in ram when the book is on the home screen, so occasionally updating the cover doesn't take effect right away. A reboot of the device will fix that, but eventually it picks up the new cover without a reboot or remove/re-add.
I can't think of any other meta-data special cases, but I'm sure there are some.
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