My experience with KOReader is that it opens and reads updated books with new chapters fine just by writing the new epub to the device.
However, it doesn't automatically update the cached metadata displayed in it's file browser, if any of that's changed.
The only reason I know anything about it is I've just this last week been switching to KOReader on Kobo. Due to all the extra steps necessary for Kobo's native software (aka Nickel), I decided to disable the KoboTouch and use the User Defined USB device instead. Some discussion
over here.