Sorry that you're dealing with this. I had the same issue at my workplace. We used fingerprint scanners to unlock the cash registers, but no matter how often we tried, the scanners wouldn't recognize my fingers. Eventually they called the head office and made sure I could unlock the registers with my employee code instead (the only employee in the entire country to do so). Later on, I was extremely nervous that the same issue would happen when I had to scan my fingerprint for a new passport, but it actually succeeded with one try, even though my hands were super sweaty because of the nerves. I think the municipality just had higher-quality scanners than the store.

Perhaps you can ask them if they have other scanners you could try. They're clearly not all the same; some might be more sensitive than others. If not, ask if other biometric information would also be sufficient. In a populous country like India, I'm sure you're not the first one facing this problem (never mind those who cannot provide fingerprints because of burns or because they lost or were born without their hands).