Add-Type -Path "C:Microsoft.SharePoint.Client.dll"
Add-Type -Path "C:Microsoft.SharePoint.Client.Runtime.dll"

$username = "name@domain.com"
$password = "<password here>”
$srcUrl = "<enter the source Url>" ## use the full URL of the site
$destUrl = "<enter the target Url>" ## use the full URL of the site
$srcLibrary = "<Lib Name>"
$destLibrary = "<Target Lib>"
$destinationFolder = "/sites/<SITENAME>/Shared Documents/<folder inside doc lib>/" ## Make sure the folder name ends with /

$securePassword = ConvertTo-SecureString $password -AsPlainText -Force
$credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($username, $securePassword)


function CreateFolders
{
    param (
        [Parameter(Mandatory=$true)] $srcfolder,
        [Parameter(Mandatory=$true)] [string] $destFolderPath
    )

    Write-Host "Source Folder:" + $srcfolder.Name + " dest folder:" + $destFolderPath -ForegroundColor Yellow
    $SPOFolder = $destWeb.GetFolderByServerRelativeUrl($destFolderPath)
    $FolderName = $srcfolder.Name
    $NewFolder = $SPOFolder.Folders.Add($FolderName)
    $destWeb.Context.Load($NewFolder)
    $destWeb.Context.ExecuteQuery()
    Write-Host "Folder Created - " + $FolderName -ForegroundColor Yellow

    ## get source folder details
    $SrcFolderListItem = $srcfolder.ListItemAllFields
    $srcContext.Load($SrcFolderListItem)
    $srcContext.ExecuteQuery()
    ####

    $SPOFolderItem = $NewFolder.ListItemAllFields;
    $replacedUser =$destWeb.EnsureUser($SrcFolderListItem["Editor"].Email)
    $SPOFolderItem["Editor"] = $replacedUser
    $replacedUser =$destWeb.EnsureUser($SrcFolderListItem["Author"].Email)
    $SPOFolderItem["Author"] = $replacedUser
    $SPOFolderItem["Created"] = $SrcFolderListItem["Created"]
    $SPOFolderItem["Modified"] = $SrcFolderListItem["Modified"]
    $SPOFolderItem.Update()
    $destContext.Load($NewFolder)
    $destContext.ExecuteQuery()

    $fileCol = $srcfolder.Files
    $srcContext.Load($fileCol)
    $srcContext.ExecuteQuery()

    ### Load the file to hash table to check with Target library.
    $hashFiles = @{}
    $DestfileCol = $NewFolder.Files
    $destContext.Load($DestfileCol)
    $destContext.ExecuteQuery()
    foreach ($destFile in $DestfileCol){
        $hashFiles.add($destFile.Name,$destFile.Name)
    }

    foreach ($f in $fileCol)
    {
        if($hashFiles.ContainsKey($f.Name) -ne "true")
        {
            $srcContext.Load($f)
            $srcContext.ExecuteQuery()
            $id = $srcfolder.Name
            $nLocation =$NewFolder.ServerRelativeUrl.TrimEnd("/") + "/" + $f.Name
            Write-Host $nLocation

            try
            {
                $fileInfo = [Microsoft.SharePoint.Client.File]::OpenBinaryDirect($srcContext, $f.ServerRelativeUrl)
                [Microsoft.SharePoint.Client.File]::SaveBinaryDirect($destContext, $nLocation, $fileInfo.Stream,$true)
                $ListItem = $f.ListItemAllFields
                $srcContext.Load($ListItem)
                $srcContext.ExecuteQuery()
                $fileCreated = $destWeb.GetFileByServerRelativeUrl($nLocation)
                $destContext.Load($fileCreated)
                $destContext.ExecuteQuery()
                $DestListItem = $fileCreated.ListItemAllFields;
                $replacedUser =$destWeb.EnsureUser($ListItem["Editor"].Email)
                $DestListItem["Editor"] = $replacedUser
                $replacedUser =$destWeb.EnsureUser($ListItem["Author"].Email)
                $DestListItem["Author"] = $replacedUser
                $DestListItem["Created"] = $ListItem["Created"];
                $DestListItem["Modified"] = $ListItem["Modified"];
                $DestListItem.Update()
                $destContext.Load($fileCreated)
                $destContext.ExecuteQuery()
            }
            catch
            {
                Write-Host $_ -ForegroundColor Red
            }
        }
    }

    $fL1FolderColl = $srcfolder.Folders
    $srcContext.Load($fL1FolderColl);
    $srcContext.ExecuteQuery();
    foreach ($myFolder in $fL1FolderColl)
    {
        $srcContext.Load($myFolder)
        $srcContext.ExecuteQuery()
        CreateFolders $myFolder $NewFolder.ServerRelativeUrl
    }

}

#### The main script starts here ######
$srcContext = New-Object Microsoft.SharePoint.Client.ClientContext($srcUrl)
$srcContext.Credentials = $credentials
$destContext = New-Object Microsoft.SharePoint.Client.ClientContext($destUrl)
$destContext.Credentials = $credentials
$srcWeb = $srcContext.Web
$srcList = $srcWeb.Lists.GetByTitle($srcLibrary)
$query = New-Object Microsoft.SharePoint.Client.CamlQuery
$listItems = $srcList.GetItems($query)
$srcContext.Load($srcList)
$srcContext.Load($listItems)
$srcContext.ExecuteQuery()
$destWeb = $destContext.Web
$destList = $destWeb.Lists.GetByTitle($destLibrary)
$destContext.Load($destWeb)
$destContext.Load($destList)
$destContext.ExecuteQuery()

########### this is to copy only certain folders
#$folder = $srcWeb.GetFolderByServerRelativeUrl($srcFolder)
#$srcContext.Load($folder)
#$srcContext.ExecuteQuery()
#Write-Host $destinationFolder
#CreateFolders $folder $destinationFolder
##############

foreach($item in $listItems)
{
    if($item.FileSystemObjectType -eq "File")
    {
        #$srcContext.Load($item)
        #$srcContext.ExecuteQuery()
        $srcF = $item.File
        $srcContext.Load($srcF)
        $srcContext.ExecuteQuery()
        $rootLocation = $destinationFolder + $srcF.Name
        Write-Host $rootLocation
        $fileContent = [Microsoft.SharePoint.Client.File]::OpenBinaryDirect($srcContext, $srcF.ServerRelativeUrl)
        [Microsoft.SharePoint.Client.File]::SaveBinaryDirect($destContext, $rootLocation, $fileContent.Stream,$true)
        $fItem = $srcF.ListItemAllFields
        $srcContext.Load($fItem)
        $srcContext.ExecuteQuery()
        $fCreated = $destWeb.GetFileByServerRelativeUrl($rootLocation)
        $destContext.Load($fCreated)
        $destContext.ExecuteQuery()
        $DListItem = $fCreated.ListItemAllFields;
        $replacedUser =$destWeb.EnsureUser($fItem["Editor"].Email)
        $DListItem["Editor"] = $replacedUser
        $replacedUser =$destWeb.EnsureUser($fItem["Author"].Email)
        $DListItem["Author"] = $replacedUser
        $DListItem["Created"] = $fItem["Created"];
        $DListItem["Modified"] = $fItem["Modified"];
        $DListItem.Update()
        $destContext.Load($fCreated)
        $destContext.ExecuteQuery()
    }
    elseif ($item.FileSystemObjectType -eq "Folder")
    {
        $srcContext.Load($item)
        $srcContext.ExecuteQuery()
        $folder = $srcWeb.GetFolderByServerRelativeUrl($item.FieldValues["FileRef"].ToString())
        $srcContext.Load($folder)
        $srcContext.ExecuteQuery()
        ##################
        Write-Host $destinationFolder
        CreateFolders $folder $destinationFolder
    }
}

Write-Host "Script End"