SO-41961623

Program.cs

using System.Collections.Generic;
using AutoMapper;

namespace ConsoleApplication2
{
    internal class Program
    {
        private static void Main(string[] args)
        {
            InitAutoMapper();

            var parent = new Parent
            {
                Locations = new List<Location>
                {
                    new Location
                    {
                        LocationId = 123,
                        Name = "test"
                    }
                }
            };

            var destination = Mapper.Map<Destination>(parent);
        }

        private static void InitAutoMapper()
        {
            Mapper.Initialize(
                cfg =>
                {
                    cfg.CreateMap<Location, int>().ConvertUsing(source => source.LocationId);
                    cfg.CreateMap<Parent, Destination>()
                        .ForMember(dest => dest.Locations, opts => opts.MapFrom(src => src.Locations));
                });
        }
    }

    public class Parent
    {
        public List<Location> Locations { get; set; }
    }

    public class Location
    {
        public int LocationId { get; set; }
        public string Name { get; set; }
    }

    public class Destination
    {
        public List<int> Locations { get; set; }
    }
}