Sequentially execute tasks
@echo off
taskkill /t /im App.exe
ping -n 5 127.0.0.1 > nul
xcopy /y /r "C:Some pathMy File.ext" "C:App path"
Del /f /q "C:App pathApp sub-directory*.*"

@echo off

setlocal EnableDelayedExpansion

for /f "tokens=2" %%p in ('tasklist /fi "imagename eq App.exe" /fo list ^| find "PID:"') do set pid=%%p

taskkill /t /pid %pid%

:wait
ping -n 2 127.0.0.1 >nul
tasklist /fi "pid eq %pid%" /fo list | find "PID:"
if %errorlevel% equ 0 goto wait

xcopy /y /r "C:Some pathMy File.ext" "C:App path"
del /f /q "C:App pathApp sub-directory*.*"

endlocal

Set wmi = GetObject("winmgmts://./root/cimv2")
query = "SELECT * FROM Win32_Process WHERE Name = 'App.exe'"

For Each p In wmi.ExecQuery(query)
  p.Terminate
Next

Do While wmi.ExecQuery(query).Count > 0
  WScript.Sleep 100
Loop

Set fso = CreateObject("Scripting.FileSystemObject")
If fso.FileExists("C:App pathMy File.ext") Then
  fso.DeleteFile "C:App pathMy File.ext", True
End If
fso.CopyFile "C:Some pathMy File.ext", "C:App path", True
fso.DeleteFile "C:App pathApp sub-directory*.*", True

Set f = fso.GetFile("C:App pathMy File.ext")
f.Attributes = f.Attributes And Not 1