Iwouldn't move it with any water in it. You were right the first time--empty it then refill it iwth the same water. 29g of water makes a heck of a waterfall!
Yeah but if you drain it to just a couple of inches, it's not longer 29g worth of waterfall. I'm of the opinion that its less stressful on the fish to be moved this way than to be netted, but into bucket, renetted, put into tank.
And as was said above, water contains next to none of the bacteria, it's almost all in the filter, with some in the gravel.