thanks buddy...Yes you can do that, but make sure to go into settings and straight to update when you're in emunand ONLY (so it should show GW3DS v9.X.X.). No need to format.
You can backup your sysNAND in the event you accidentally update that and not your emunand, but keep in mind the only way to restore that backup would be to do a hardware mod to your 3DS.
as Oishikatta said, updated while I was in 2.6 and a day or two before 9.4 firmware release.How are you even on 9.3? You should be going from 9.2-9.4 skipping 9.3 entirely.