I am aware of what Reese says in the first film. It was retconned for the following film (T2) and Terminator 3 that Connor had lied to Reese. The Skynet Defense Grids were smashed, that is correct, but Skynet has backup nodes that activate in the event of failure of the primary node. If you destroyed SAC-NORAD, for example, an auxiliary node would activate elsewhere - say LA since that was where the battle happened in T2. By T3 Skynet was back at CRS HQ as of 2032 according to the novelization and the script. We know from T4 that Skynet had moved to San Francisco between JD and 2018.