I am familiar with the Indian dialect of English, having spent a lot of time in India and being married to an Indian.
Having said that, I cannot imagine why "whether or not" annoyed your boss. It is a common and completely innocuous expression that should not bother anybody.
Your sentence would read as well and mean the same if you had just used "whether" instead of "whether or not." Perhaps you can find a tactful way of asking him whether that would have pleased him better (or not). Or maybe it would be best to let the sleeping dog lie.