Hi Tejitha Buddharaju,
Yes, as per the ATO you can still report and claim for FN01 if you paid your employees JobKeeper payments in that period. You will need to record the Top-Up amounts for that payrun and enter the FN01 category to advise the ATO you are claiming from this period.
As you have already processed and lodged that payrun, see this article for steps to 'back pay' the employees in your next payrun. When you finalise and lodge this pay run, the employees will have been paid $X per fortnight for each of the fortnights you are claiming the JobKeeper payment for and the ATO will be advised that you're claiming the subsidy from whatever fortnight you choose.
-Kass