after b.u.permission

flats after issuance
of completion certificate without payment of GST in terms of
clause 5 of schedule-III to CGST Act are exempt supplies 

As per section 17 . Input Tax credit is restricted to the amount as is attributable to taxable Supplies.

So , Offcourse you have to reverse the ITC claim on flat will reverse when sold after B.U permission or completion certificate.

Note: method of attribution of eligible ITC has been prescribed in Rule 42 

Yes. Flats sold after CC and for which entrire consideration is received after CC is not a supply as per GST (Schedule 3).

So as per section 17(2), Input tax credit already availed in respect of those flats are to be reversed.

Rule 42 applies. But the phrase "intended to be used" and "tax period" may create confusion on calculation when exactly followed Rule 42.