In the chronology of documents the Appointment letter is the more recent one and hence binding.
However if there is a discrepancy it has to be looked into by both the parties immediately.
If this had not been done then whatever is the latest prevails.
You have not mentioned on what basis they are asking for refund.
Are they citing Appointment letter or Offer Letter?
The above approach is based on logic.
To get a legal opinion you have to get it from Legal experts.
If I remember right there are many senior legal experts like Mr.Kargoankar and
Mr Madhu who interact in Cite HR forum. Please write to them with a personal request.