At the same time you are generating GDS, you should generate the new netlist, and you will compare the GDS with this new netlist (which was modified). The LVS will prove, that GDS and netlist are equivalent (point by point). In order to be sure, that final GDS is logically equivalent to initial netlist, you must run Formal verification between initial netlist and the final netlist. So, if init_netl==final_netl (by formal_verif) AND final_netl==final_gds (by LVS), then init_netl==final_gds. Or differently init_netll == final_netl == final_GDS. It is usual flow, there are several different flows like: use functional simulation rather the formal verification (no 100% guarantee); use derived from GDS netlist as one of inputs netlist to formal verification...