using System;

using System.Collections.Generic;

public class Program

{

    public static void Main()

    {

        var model = new Dictionary<string, Dictionary<string, Model>>

        {

            {

                "BaseKey1",

                new Dictionary<string, Model>

                {

                    {"SubKey1", new Model { Time = new DateTime(2020, 09, 15)}},

                    {"SubKey2", new Model { Time = new DateTime(2020, 12, 15) }}

                }

            },

​

            {

                "BaseKey2",

                new Dictionary<string, Model>

                {

                    {"SubKey1", new Model { Time = new DateTime(2020, 11, 15) }},

                }

            }

        };

        var result = new Dictionary<string, Model>();

        foreach (var subDictionary in model.Values)

        {

            foreach (var (key, value) in subDictionary)

            {

                if (!result.TryGetValue(key, out var existingValue) || value.Time < existingValue.Time)

                {

                    result[key] = value;

                }

            }

        }

        result.Dump();

    }

}

​

public class Model

{

    public DateTime Time { get; set; }

    public override string ToString() => Time.ToString();

}