GPS? Not likely. A 50 MT weapon would generate irradiance on the order 10 W/m^2 at GPS satellite altitudes (I = E/(4*pi*r^2)). The irradiance from the sun incident on satellites in the Earth sphere is roughly 1400 W/m^2, not including particle bombardment outside of the radiation belt; you can imagine the tolerances built into our sats to withstand that kind of punishment. My understanding is EMP launchers are sub-orbital--LEO. Nobody can launch one into GTO without somebody noticing, and if the Chinese have ASAT that can reliably strike up that high we're screwed no matter which way you slice it.
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