I do that all the time with no issues. I probably do it more with the built-in KoboTouch driver, but, it has definitely worked with the KoboTouchExtended driver several times in the last week or so.
In the driver configuration, do you have the "Silently Ignore Failed Conversions" turned on? If so, if there was a problem with the change to kepub, the book won't be sent. But, it doesn't explain why it was sent after deleting the book. At this point, it is probably to late to see what happened. A debug log would probably give an idea of what happened. If it happens again, can you run calibre in debug mode and send the book to the device by itself. Then post the log and I'll have a look at it.
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