Kindly see sub-section 10 of Section 54 of the CGST Act, 2017, which reads as under:
"Where any refund is due 7[****] to a registered person who has defaulted in furnishing any return or who is required to pay any tax, interest or penalty, which has not been stayed by any court, Tribunal or Appellate Authority by the specified date, the proper officer may-
(a) withhold payment of refund due until the said person has furnished the return or paid the tax, interest or penalty, as the case may be;
(b) deduct from the refund due, any tax, interest, penalty, fee or any other amount which the taxable person is liable to pay but which remains unpaid under this Act or under the existing law.
Explanation.––For the purposes of this sub-section, the expression “specified date” shall mean the last date for filing an appeal under this Act."
In view of above provision, Dept. sought to give you other eligible refund-claim in your situation.
I am not sure if I understood what is real problem and valid legal reasons behind such problem (if any), which you facing. May you please elaborate.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.