Just to confirm: it worked very well for me. I added the following line at the very end of the config file classicthesis-config-LyX.tex (working with LyX)
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\usepackage[left=3.5cm,right=2.5cm,top=3cm,bottom=2.5cm]{geometry}
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\usepackage[left=3.5cm,right=2.5cm,top=3cm,bottom=2.5cm]{geometry}