Gst refund

a private company has received some advance of Rs.19 lacs in jan 2019 against sell of computer systems
on this amount of advance the gst was deposited as CGST and SGST considering it as intra state sale transaction but later on at the time of invoicing in March 2019 it was found that the purchaser's gstin is registered in different state so igst was charged in the final invoice of rs 29 lacs
now the problem is the amount already deposited as cgst sgst
the same amount could not be shown against this invoice .
what to do in this matter
please suggest