Circular No.135/05/2020 - GST dated 31.03.2020 was issued by CBIC in exercise of its powers conferred by section 168 (1) of the Central Goods and Services Tax Act, 2017 and thereby, these are binding instructions which Dept's officer has to follow.
However, in Para 5 of said circular, it is clearly seen that CBIC has changed its policy (i.e. to grant refund only against ITC whose invoices are reflected in GSTR-2A) due to insertion of sub-rule (4) to rule 36 of the CGST Rules, 2017 vide notification No. 49/2019-GST dated 09.10.2019.
As querist has clarified that subject refund-claim was for Sept, 2019, one can argue that changes brought vide Circular No.135/05/2020 - GST dated 31.03.2020 cannot be applied to subject refund-claim. (However, Dept. may claim / argue that date of taking ITC is actual date of filing of GSTR-3B for Sept, 19 ..... another controversy under GST)
But more importantly, Para 5 of said circular clearly overrides relevant legal provisions allowing refund of accumulated ITC. And thereby, it is fit case to challenge said instructions of Para 5 (& SCN so issued) by filing writ petition in jurisdictional high Court.
It is ironical that in Para 2.2 of very same circular, CBIC notes that 'Hon’ble Delhi High Court vide para 12 of the aforesaid Order has observed that the Circulars can supplant but not supplement the law. Circulars might mitigate rigours of law by granting administrative relief beyond relevant provisions of the statute, however, Central Government is not empowered to withdraw benefits or impose stricter conditions than postulated by the law' and then CBICgoes on given more instructions to its officers in Para 5 which are nothing but withdrawing benefits or imposing stricter conditions than postulated by the law'.
From query, it seems that Dept. is seeking only recovery of refund already granted but not sought denial of ITC. Unless ITC itself is denied, refund thereto cannot be denied in given situation under discussion. And this fact will make 'grounds to be taken in suggested writ petition' more forceful.
Al above are strictly my personal views and same should not be taken as professional advice / suggestion.