Glengarry5,
Sadly I know of no singular online resource. I have a plan to create my own excuse for one on my hobby site -- maiwandday.com -- but it won't become a reality for some time yet. Meanwhile I advise you to search via Google or whatever search engine you prefer, as there are period photos and illustrations featuring regimental flags of a handful of British Indian Regiments from approximately c.1860 to 1900 online. Of course these don't all date specifically to the 1878-1880 Second Afghan War, but at least they are close. I am slammed with "Real World" work at the moment or I'd try to track down and repost here that same handful of online images, but here's a list of regiments whose colours I've seen photos or illustrations of on the web with my own eyes:
1st Bengal light Infantry
8th Bengal Native Infantry
15th Ludhiana Sikhs
16th Punjabis
29th Bengal Native Infantry
30th Punjabis
62nd Punjabis
80th Carnatic Infantry
Here's the picture of the 15th Ludhiana Sikhs -- which is a bit frustrating for use as painting reference but IMHO still useful :
…and here's the 52nd Sikhs:
Again, neither of the above images date to the Second Afghan War but as regimental colours were not retired unless or until they'd been reduced to virtual shreds, or made obsolete by amalgamation with other regiments, even if you are a grognard button-counter type they are potentially useful.
WHOOPS -- almost forgot these 2 shots from way back in 2010 when I did my 140th Anniversary Maiwand Day game…
30th Bombay Native Infantry (Jacob's Rifles):
…and 1st Bombay Native Infantry (Grenadiers):