I assume you never go into nickel? If so, you are seeing the result of fixing a bug in how the KoboTouch driver finds books on the device.
The KoboTouch driver uses the database on the device to find books. Anything not in the database is ignored. During the processing, anything that is in the metadata.calibre that is not in the database is also removed. If you use the driver, you need to let nickel process the books into the database.
If you are only using Koreader, then I suggest disabling the KoboTouch driver and connecting to the device as a Folder Device. This does a scan of the device to find all know books and will maintain the metadata.calibre in whatever directory you connect to as the root.
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