What I should do, I have purchased some shares in NSE and some in BSE for the same company in Zerodha, now all shares are showing in NSE on the Zerodha kite app and the prices on NSE are less than the BSE, so my all holdings are at a loss?

That is default way of showing in Zerodha as NSE is more active in terms of trade then BSE.

The stocks ate not exchange specific if traded by delivery. If they are traded same day then you have sell in same exchange.

So, just select the higher prices exchange and sell in it.

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