You need to extend the theme, not overwrite it.
module.exports = {
mode: "jit",
purge: ["./pages/**/*.{js,ts,jsx,tsx}", "./components/**/*.{js,ts,jsx,tsx}"],
darkMode: false,
theme: {
extend: {
colors: {
transparent: "transparent",
current: "currentColor",
primary: {
superlight: "#FFFFFF",
light: "#FFF8F0",
DEFAULT: "#FFEBD1",
dark: "#978F85"
},
secondary: {
light: "#EFEFEF",
DEFAULT: "#A0A0A0",
dark: "#26221D"
}
}
}
},
variants: {
extend: {}
},
plugins: []
};
Also, keep in mind that JIT mode is still not completely bug-free. If you experience issues like that again, try restarting your server.
Hope this helps!