That only happened in the Stirling T2 novels. None of the canon Terminator stuff has actually gone into detail about what military assets survived in any usable form. Even this show hasn't; the mention of the Carter and the glimpse of the carrier in "Allison from Palmdale" are just background things that don't tell us much about the overall disposition of either sides' assets.All United States Navy vessels were reprogrammed and upgraded with cybernetic brains following the break through to the Skynet System. On JD Skynet shut down the environmental systems of the subs and took over them by remote.