@echo off
set "SrcFolder1=D:\A"
set "SrcFolder2=D:\B"
set "DstFolder=E:\B"

for /r "%SrcFolder2%\" %%i in (*) do (
    set "file=%%i"
    setlocal enabledelayedexpansion
    if not exist "!file:%SrcFolder2%=%SrcFolder1%!" (
        for %%j in ("!file:%SrcFolder2%=%DstFolder%!") do (
            endlocal
            md "%%~dpj" 2>nul
            copy "%%i" "%%~dpj"
        )
    ) else endlocal
)
pause
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