As long as your salinity and pH are the same they should be alright. There is very little if any good bacteria in your water if I remember right. (Someone please correct me if I'm wrong!)
I recently upgraded as you are doing right now and used new sand. I didn't use any of the old water as I was told that it has no beneficial bacteria in it. I just simply moved all the rock over first then all my livestock.
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I am going to be moving everything from my Biocube to my new 60 gallon. I am going to do new sand and just use my exiting rock for now. If I use the water from my biocube and fill the rest with new water, would that be too stressful for the livestock?
Any updates Joe?