If you have a custom theme installed, make sure to uninstall it (via NXThemesInstaller) before you proceed to update.
Whenever you're about to update your firmware and before you do so, make sure that both Hekate and Atmosphere support the...
In hekate, under tools there is a button with something like "bit fix" ( sorry, but I don't have the switch right now ). It worked for me when I cloned the old SD into the new one.
Give it a try.