A customer asked for a refund and the reason given was “ order not received”

What happens in the case of FBA as a refund has been initiated by Amazon, how can I see if the item is back in my inventory or not, maybe the customer received yet claimed not received !

In that case I lost money plus item both?

The best way to handle this at scale is a service like getida or seller investigators. I use both.

Yes, that happens.

Can’t I open case with Amazon to ask for money or any way I can check in my account item is back? I doubt, the customer received it but saying not received.

You can check with them. Amazon is here to make the customer happy, sometimes at your expense.