I'm assuming here that you are talking about the Native regiments. FWIW, a quick look through the venerable (if not always reliable) "Military Flags of the World" by Terry Wise, suggests that, prior to 1781 when the two-colour system of the British Army was adopted, each of the Presidency armies had its own system (somewhat less than helpfully, he supplies no illustrations). Bengal had a single flag per company in the facing colour with a regimental device in the centre; the grenadier company also had the Union flag in the canton. Madras had a red cross of St George on a coloured field, according to regiment/battalion. Nothing for Bombay. It is tempting to think that the two-colour system would have involved the Company flag as the equivalent of the King's Colour, but I could find nothing to support that. Unfortunately, CCP Lawson's work on British Army uniforms and flags stops short of the HEIC, despite including information on Swiss troops raised for service in India.