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Ok, provided the clutch is completely released and you are currently in 3rd gear...
There is no input from the engine, so the output shaft will be driven by the rolling wheels. At this point this is your only source of incoming force into the transmission. The output shaft will be driving the input shaft, which is spinning close to whatever RPM the engine was at when you released the clutch. At this point whenever you upshift, the synchros have the wonderful job of slowing all the rotating mass of the input shaft and all the gears riding on it to the speed dictated by the new gear ratio. So if you are at say 60 mph in 3rd and shift to 6th the input shaft will have to slow from ~6000rpm to ~2700rpm. Now if you were in 5th gear at 60mph and shifted into 6th the drop would only be from ~3600rpm to ~2700rpm, quite a bit less energy to dissipate. So the skip-shifting means more energy dissipation which is more heat generated which is more wear created. Seeing as the equation for rotational kinetic energy is: (1/2)*I*omega^2, where omega is your angular velocity (RPMs). It would seem going from the 5th-6th shift of 900rpm drop to a 3rd-6th shift with a drop of 3300rpms would result in having to dissipate 7 times the amount of energy as a normal shift! So instead of your 6th gear synchro lasting, oh say 210,000 miles, it would only last 30,000 miles!
Now that is entirely a theoretical discussion and real life is infinitely more complex than what is represented above, your shifting habits, the type of MTF your run, and even the speed at which you skip-shift among many others will all affect the mileage you get from your transmission.
The safest bet, double clutch your upshift if you are going to be skipping that many gears. And if you don't, as long as these aren't redline skip shifts under high load, you should be ok.
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