Receipt of Fund

Till ,I know,there is no prohibition in this regard ,Subject to Company Y is not a Related party to your company in anyway ,However ,Even for precautions ,You should Issue Invoice In name of Company Y ,While Company X will be shown as Consignee to order ,If invoice is already issued ,then for safe side ,you can come into agreement with Y ,or issue debit note to Y ,clearly indicating Name of consignee , Descripttion of goods ,qty,payable amount ,etc.duly acknowledged by Company Y's authd. person ...