Two different visa on two different country passport - birth countrys different

Hi Experts,

I have a serious question which needs experts advise:

I am Nepali and have Nepali passport working in India over one decade. My wife is Indian and has Indian passport.

We have received Indian passport for my son (age: 13 years) which contains his birth place is in India. My son and wife got L2 Visa stamped on their passports but they did not travel due to family reason. Now our visas are expired.

Last month we received Nepali passport for my son which denotes his place of birth is in Nepal. We don’t want to use his Indian passport which is still valid and want to discard it for forever.

My question is, if I submit my son’s new Passport (i.e. Nepali passport) for H4 visa stamping in India (since I have H1B visa now) -

will they (immigration department) ask clarification why my son has two different countries passports ( because their database will have all his record collected during L2 stamping) ?Will they raise question why the place birth is different in two different passports ?Will they ask me to provide any official proof/document which would explain that we have discarded his Indian passport for forever and will not use them again.Honestly speaking, I feel guilt over my son’s dual passport. What should I do to not make my son’s future dark, specially, w.r.t. the USA immigration.

Can someone guide me in this matter please ?

Thank you in advance !