In addition to the 66th Berkshires, some sources also mention the 1st Bombay Grenadiers losing their Regimental Standards at the battle of Maiwand.
On the other hand, though there are photos and illustrations showing various Indian infantry units with their regimental standards before and after the Second Afghan War, I don't think I've ever seen one from the war itself. Of course I'm no authority, and such photos or illustrations may well exist (and hopefully might be posted in this thread!) but if they don't, it doesn't mean Indian Infantry Regiments never carried their standards with them during the Second Afghan War.
Speaking for myself, I will continue to field regimental standards with my Second Afghan War Indian infantry units, since there's no absolute proof (at least that I know of) that they weren't and... they just look good.
MIKE OWEN: I humbly ask you to PLEASE INCLUDE STANDARD-BEARERS IN YOUR ARTIZAN SIKH & PUNJABI COMMAND PACKS, so I don't have to convert them the way I did with my Perry Sudan Sikh and Bengal/Bombay Infantry Command Packs!