Transiting thru India without a visa & a 2 hour connection is a bit of risk. Not sure what the timatic rule is on this, but for the most part, a lot of the ground staff are clueless when it comes to slightly complex situations such as the above. Your in luck if you have access to a supervisor on duty who knows the system well enough to help out.

Would have been best to sort out the visa before leaving, that way there would have been a PLAN B to fall back on.