SQL Concurrent Inserts and Automatically Find Active Flag Record
Based on the question 'What is the proper database design':

Having a 'CurrentFlag' column 'de-normalises' the schema design a little, for the sake of identifying the current order for a customer quickly. 

I've worked on databases that use this method, but it is a performance trade-off that requires 'code' (e.g. triggers) to maintain the column.
This is where concurrency issues can creep in because of the extra work being done upon insert.

However, the same result can be achieved without changing the schema, by adding a descending order covering index which 'includes' the 'CustomerOrderID' in the index itself.

Testing is required for this index-only solution to ensure it is performant under the '100 million inserts in week time span' load, especially when querying the data (see end of the code sample).

Covering index example code:

--Create a test table for the example based on given schema
USE [testDB]
GO

SET ANSI_NULLS ON
GO

SET QUOTED_IDENTIFIER ON
GO

CREATE TABLE [dbo].[CustomerOrder](
    [CustomerOrderId] [bigint] IDENTITY(1,1) NOT NULL,
    [CustomerId] [int] NOT NULL,
    [FileLastModified] [datetime] NOT NULL,
    [Productsku] [varchar](25) NOT NULL,
    [Quantity] [int] NOT NULL,
 CONSTRAINT [PK_CustomerOrder] PRIMARY KEY CLUSTERED 
(
    [CustomerOrderId] ASC
)WITH (PAD_INDEX = OFF, STATISTICS_NORECOMPUTE = OFF, IGNORE_DUP_KEY = OFF, ALLOW_ROW_LOCKS = ON, ALLOW_PAGE_LOCKS = ON) ON [PRIMARY]
) ON [PRIMARY]
GO

-- Create the covering index
CREATE NONCLUSTERED INDEX IX_ActiveCustomerOrder 
    ON dbo.CustomerOrder (CustomerID ASC, FileLastModified DESC) INCLUDE (CustomerOrderID);

-- Insert dummy data (with dates out of order)
INSERT INTO [dbo].[CustomerOrder] ([CustomerId] ,[FileLastModified] ,[Productsku] ,[Quantity]) 
       VALUES (100, '17-Oct-2017', 'Prod1',20);
INSERT INTO [dbo].[CustomerOrder] ([CustomerId] ,[FileLastModified] ,[Productsku] ,[Quantity]) 
       VALUES (100, '15-Oct-2017', 'Prod1',30);
INSERT INTO [dbo].[CustomerOrder] ([CustomerId] ,[FileLastModified] ,[Productsku] ,[Quantity]) 
       VALUES (100, '18-Oct-2017', 'Prod1',41);
INSERT INTO [dbo].[CustomerOrder] ([CustomerId] ,[FileLastModified] ,[Productsku] ,[Quantity]) 
       VALUES (100, '14-Oct-2017', 'Prod1',42);
INSERT INTO [dbo].[CustomerOrder] ([CustomerId] ,[FileLastModified] ,[Productsku] ,[Quantity]) 
       VALUES (100, '13-Oct-2017', 'Prod1',43);


-- Fetch the active order for a single customer using an index hint
SELECT TOP(1) CustomerID, CustomerOrderId, [FileLastModified] 
FROM dbo.CustomerOrder WITH (INDEX=IX_ActiveCustomerOrder)
    WHERE CustomerID = 100; 

-- Fetch active orders for all customers
SELECT x.CustomerID, x.CustomerOrderId, x.[FileLastModified]
FROM (
SELECT CustomerID, 
       CustomerOrderId, 
       FileLastModified, 
      (ROW_NUMBER() OVER(PARTITION BY CustomerID 
                    ORDER BY FileLastModified DESC)) AS RowID 
  FROM dbo.CustomerOrder WITH (INDEX=IX_ActiveCustomerOrder)
) x
WHERE x.rowid = 1;