Between branches of the company ,supply made ,but no payments are made

Under earlier law, we used to do branch transfers against form f. But under gst , since it amounts to supply , we are raising the tax invoice and discharging the gst liability. but with regard invoice payment , how do we do.?since it is the same company under one PAN payments are not getting effected. In absence of the same ,does it amount to disallowance of input gst that was claimed from month to month?. kindly advise.