I'm glad Victory came through with a replacement bike! At least they followed through on supporting their customer in the end.
Clutchless shifting shouldn't cause any significant damage, provided you use the right technique. Most motorcycles (and I'm almost certain the IET transmission in the Empulse is one of them) use a constant mesh sequential transmission. That means all of the gears are meshed all of the time, but not connected to the output shaft until a "dog clutch" engages them. The dog clutch is what you direct with your foot, and locks the correct gear to the shaft. This video has a good visual explanation, it's difficult to conceptualize:
As a result, these transmissions don't "grind" in the same way a car's transmission does. The force of the shift is to the dog clutch, a robust part, and these types of transmissions are routinely shifted without a clutch in performance applications. The key technique is to engage the dog clutch when the transmission is unloaded, i.e. off throttle, and shift firmly and quickly. Quick shifters can do this by cutting spark for the miniscule amount of time it takes to slide into the next gear. Humans have to do it with a flick of the wrist
Here's more info on the Empulse transmission if anyone's interested:
http://www.ietspa.com/portfolio-posts/iet/TL;DR Clutchless shifting is fine if you shift when there is little load on the transmission and you shift firmly. Shifting with torque on the transmission could cause damage to the dog clutches eventually. The clutch only makes sure the transmission is unloaded during a shift.