Looks like you're modifying the internal pilot textures in the cockpit zip folder. They're 2 different ones.
Materials for external pilot are
{"pilot_L39_01", 0 ,"pilot_L39",true}; -- false if texture in livery folder
{"pilot_L39_01", 2 ,"pilot_L39_spec",true};
{"pilot_L39_01", DECAL ,"empty",true};
and the default pilot texture is pilot_L39.dds in "CoreMods/aircraft/L-39/Textures/L-39_C.zip".