IMAGE_FILE_LARGE_ADDRESS_AWARE и переключатель ОС на 3 ГБ

Вы можете сделать что-то вроде этого - вам нужно передать оба пути в ProcessFolders

Sub ExcelPlot()

    Dim sourceFolder As String, destFolder As String

    With Application.FileDialog(msoFileDialogFolderPicker)
        .AllowMultiSelect = False
        .Title = "Locate the Excel files"
        If .Show = -1 Then
            sourceFolder = .SelectedItems(1)
            .Title = "Where would you like to save the PDFs?"
            If .Show = -1 Then
                destFolder = .SelectedItems(1)
                ProcessFolders sourceFolder, destFolder
                Shell "Explorer.exe" & " " & destFolder, vbNormalFocus
            End If
        End If
    End With
End Sub

РЕДАКТИРОВАТЬ: Вот обновленная (не рекурсивная) версия вашей подпрограммы обработки папок: [114 ]

Sub ProcessFolders(sourceFolder As String, destFolder As String)

    Dim objFileSystem As Object
    Dim objFolder As Object
    Dim objSubFolder As Object
    Dim objFile As Object
    Dim objWorkbook As Excel.Workbook
    Dim strWorkbookName As String, strFileExtension As String

    Set objFileSystem = CreateObject("Scripting.FileSystemObject")
    Dim colFolders As New Collection

    colFolders.Add sourceFolder

    Do While colFolders.Count > 0

        Set objFolder = objFileSystem.GetFolder(colFolders(1)) 'get the first path
        colFolders.Remove 1 'remove from listing

        'Process files in this folder
        For Each objFile In objFolder.Files

            strFileExtension = objFileSystem.GetExtensionName(objFile)
            If LCase(strFileExtension) = "xls" Or LCase(strFileExtension) = "xlsx" Then

               Set objWorkbook = Application.Workbooks.Open(objFile.Path)

               strWorkbookName = Left(objWorkbook.Name, _
                                     (Len(objWorkbook.Name) - Len(strFileExtension)) - 1)
               objWorkbook.ExportAsFixedFormat Type:=xlTypePDF, _
                  Filename:=objFileSystem.buildpath(destFolder, strWorkbookName & ".pdf")

               objWorkbook.Close False
            End If
        Next

        'Process subfolders
        For Each objSubFolder In objFolder.SubFolders
            If ((objSubFolder.Attributes And 2) = 0) And ((objSubFolder.Attributes And 4) = 0) Then
               colFolders.Add objSubFolder.Path  'add this to the collection for processing
            End If
        Next

    Loop

End Sub