I have exactly the same question in my mind, especially after doing a mess moving the same folder to a new computer, which meant GS doubled every listing with auto-restart feature enabled… it was a mess, but I hope I fixed it deleting GS from one computer. The idea of sync worries me a bit… I am doing a complicated scheme of folder, is it wasted time? I hope not… for now I suppose the only solution is using 2 separate (and totally different) applications, but of course it is a bit annoying if I use only 1 for orders… anyway, we talked about it here: Now Available? Syncing GS Between Multiple Computers? and I am still hoping in that “months” 
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