This mod is config-based. If you want to remove a map from the roster (or change the assigned levels to it), you need to make an edit in an XComMaps.ini file.

This is an example config line that adds the "Sunrise" lighting map to both Subway and Sewer levels.


If you want to remove a specific map altogether, you only need to delete the relevant line, or put a semicolon (;) before it (works like a toggle).

SETTINGS EXPLANATION:

As an alternative, I assume you would likely want to change the assigned levels to the map, or replace the map name.
Here are the relevant settings for this:

MapName: Filename of the lighting map.

Map names used in this mod:
EnvLighting_Day: sunny day with some overcast clouds.
EnvLighting_Vortex: bright, gleaming sunset with sandy colors.
EnvLighting_Sunrise: early sunrise.
EnvLighting_Sunset: late afternoon sunset with afterglow.
EnvLighting_Aerial: late midday with some clouds. Similar colors to Vortex map.
EnvLighting_UrbanNight: urban night with bluish tones.
EnvLighting_PastelDay: warmer colored variant of EnvLighting_Day.
EnvLighting_StrongholdLeadup: dim, moody subterranean lighting with warm colors (to be used with tunnel maps only).
EnvLighting_GP_Forge: bright night variant with cold colors.
EnvLighting_Day_WrapUp_Templar: dusk variant with psionic-like, otherwordly hue.
EnvLighting_Shanty_Day: sunny day with clouds and some fog.
EnvLighting_Snow_Tundra: overcast day with fog. Mild Silent Hill vibes.
XP_LE_AbandonedCity_Night_Dark: darker variant of the vanilla Nightime Abandoned City lighting.
CIN_XP_LE_UrbanNight_WrapupReaper: dark urban night.
XP_LE_Shell_Intro: gloomy, overcast night.
XP_LE_Shell_AC_Lost: pitch dark night with greenish thick fog. Disabled by default.

I also recommend the Show Lighting Map Name mod if you want to preview the map names in tactical.

arrPlotTypes: In this setting you are listing all level types you want a lighting map to work with, one by one.
The order goes from 0, to 1, 2, 3, and so on, e.g.
This example adds two mission types to the lighting map: Subway and Sewer.
Order of the added plot type names doesn't matter. Only the numbers count.

Relevant mission types:
CityCenter: self-explanatory.
Slums: self-explanatory.
Wilderness: e.g. forest levels with alien facilities/blacksites, or Avenger Defense.
SmallTown: self-explanatory.
Shanty: Resistance hideouts (retaliation)
Rooftops: Psionic Network rooftop mission.
Tunnels_Subway: self-explanatory.
Tunnels_Sewer: self-explanatory.
Abandoned: Lost Abandoned City levels.

arrBiomeTypes: There are four biomes that can be applied to SmallTown, Wilderness and Shanty missions: Temperate, Arid, Tundra, Xenoform.
Just like with arrPlotTypes, you list the biomes you want the lighting map to work with, one by one: starting from [0] and going up to [3] (because you can apply up to four biomes). Order of the added biomes doesn't matter. Only the numbers count.

Less important settings:
eEnvLighting: Assigned tag: day or night. Might influence the brightness of light fixtures. Other than that, no need to change it. Do not confuse this setting with the MapName setting.
eTimeOfDay: Assigned time of day for Geoscape mission purposes.
Accepted values: eTimeOfDay_Noon, eTimeOfDay_Dawn, eTimeOfDay_Dusk, eTimeofDay_Sunset, eTimeOfDay_Night
"Night" setting will also enable XCOM flashlight during combat sequences.
eMood: No need to change it.
eWeatherCondition: either eWeatherType_Clear or eWeatherType_Rain. Maps with rain use the latter tag. A map does not need the "Rain" tag to have a chance of raining, but it may be prioritized over maps with the "Clear" tag when the rainy map is being picked for the mission.

I recommend robojumper's Config Checker when searching for any config errors.
https://robojumper.github.io/ue3-config-parser/index.html

Also make sure the following header is already present before the config setting lines:

Otherwise, the settings will not be registered.