Recursively moves files in directory tree to/from SFTP/FTP server while preserving source directory structure

The upload examples rely on Session.TranslateLocalPathToRemote which will be available in the upcoming WinSCP 5.8.3. You can implement your alternative instead meanwhile.

Use the DirectoryInfo.EnumerateFileSystemInfos method to walk the source local tree.

using System;
using System.Collections.Generic;
using System.IO;
using WinSCP;
 
class Example
{
    public static int Main()
    {
        try
        {
            // Setup session options
            SessionOptions sessionOptions = new SessionOptions
            {
                Protocol = Protocol.Sftp,
                HostName = "example.com",
                UserName = "user",
                Password = "mypassword",
                SshHostKeyFingerprint = "ssh-rsa 2048 xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx"
            };
 
            string localPath = @"C:\data";
            string remotePath = "/home/user/backup";
 
            using (Session session = new Session())
            {
                // Connect
                session.Open(sessionOptions);
 
                // Enumerate files and directories to upload
                IEnumerable<FileSystemInfo> fileInfos = new DirectoryInfo(localPath).EnumerateFileSystemInfos("*", SearchOption.AllDirectories);
 
                foreach (FileSystemInfo fileInfo in fileInfos)
                {
                    string remoteFilePath = session.TranslateLocalPathToRemote(fileInfo.FullName, localPath, remotePath);
                    if (fileInfo.Attributes.HasFlag(FileAttributes.Directory))
                    {
                        // Create remote subdirectory, if it does not exist yet
                        if (!session.FileExists(remoteFilePath))
                        {
                            session.CreateDirectory(remoteFilePath);
                        }
                    }
                    else
                    {
                        Console.WriteLine(string.Format("Moving file {0}...", fileInfo.FullName));
                        // Upload file and remove original
                        session.PutFiles(fileInfo.FullName, remoteFilePath, true).Check();
                    }
                }
            }
 
            return 0;
        }
        catch (Exception e)
        {
            Console.WriteLine("Error: {0}", e);
            return 1;
        }
    }
}