My client paid ₹1,000, and their bank charged them a 2% fee. How does that affect me?

It doesn’t; you still receive your payment minus:

• MDR (e.g., 3% = ₹30)
• GST on MDR (e.g., ₹5.40)

➡️ Final settlement: ₹964.60

Any fees charged by your client’s bank (like a 2% card fee) are between them and their bank.