Can't delete WindowsApps and other backup folders from storage drive

I recently created a backup or restore point (im not sure which at this point) But it has created several folders, namely: Program Files, WindowsApps and WpSystem, all of which are in my secondary hard drive. Windows does not recognize that I have a backup (or some remains of, I may have cancelled the backup partway through the process) in the control panel or in any backup or restore options. I have tried to force delete these files using cmd, powershell, transferring ownership, however i cannot delete them as they are either not found (in the command prompt) or are in use by SYSTEM. Any idea how I can delete these folders?

Check disk for filesystem errors by executing Chkdsk X: /f command. Replace X: drive letter with secondary hard drive.

Take ownership of the folders you want to delete this batch script adds Take ownership to context menu.

Code:

@Echo Off


REM  --> Check for permissions
Reg query "HKU\S-1-5-19\Environment" 
REM --> If error flag set, we do not have admin.
if %errorlevel% NEQ 0 (
ECHO                 **************************************
ECHO                  Running Admin shell... Please wait...
ECHO                 **************************************

    goto UACPrompt
) else ( goto gotAdmin )

:UACPrompt
    echo Set UAC = CreateObject^("Shell.Application"^) > "%temp%\getadmin.vbs"
    set params = "%*:"=""
    echo UAC.ShellExecute "cmd.exe", "/c ""%~s0"" %params%", "", "runas", 1 >> "%temp%\getadmin.vbs"

    "%temp%\getadmin.vbs"
    del "%temp%\getadmin.vbs"
    exit /B


:gotAdmin

Cls & Mode CON  LINES=11 COLS=104 & Color 0E & Title Created By FreeBooter
Echo.
Echo.
Echo.
Echo.       
Echo         Do You Want To Add Take Ownership to the Right-Click Menu in Windows Explorer (Y/N)?    
Echo.       
Echo.
Echo.


Set /p input= RESPONSE: 

If /i  Not %input%==Y (Goto :_Ex) Else (Goto :_Start) 

:_Ex
If /i Not %input%==N  (Goto :EOF) Else (Goto :_RegRestore)



:_Start

Reg.exe add "HKCR\*\shell\runas" /ve /t REG_SZ /d "Take Ownership" /f > Nul
Reg.exe add "HKCR\*\shell\runas" /v "NoWorkingDirectory" /t REG_SZ /d "" /f > Nul
Reg.exe add "HKCR\*\shell\runas\command" /ve /t REG_SZ /d "cmd.exe /c takeown /f \"%%1\" && icacls \"%%1\" /grant administrators:F" /f > Nul
Reg.exe add "HKCR\*\shell\runas\command" /v "IsolatedCommand" /t REG_SZ /d "cmd.exe /c takeown /f \"%%1\" && icacls \"%%1\" /grant administrators:F" /f > Nul
Reg.exe add "HKCR\Directory\shell\runas" /ve /t REG_SZ /d "Take Ownership" /f > Nul
Reg.exe add "HKCR\Directory\shell\runas" /v "NoWorkingDirectory" /t REG_SZ /d "" /f > Nul
Reg.exe add "HKCR\Directory\shell\runas\command" /ve /t REG_SZ /d "cmd.exe /c takeown /f \"%%1\" /r /d y && icacls \"%%1\" /grant administrators:F /t" /f > Nul 
Reg.exe add "HKCR\Directory\shell\runas\command" /v "IsolatedCommand" /t REG_SZ /d "cmd.exe /c takeown /f \"%%1\" /r /d y && icacls \"%%1\" /grant administrators:F /t" /f > Nul


Cls & Mode CON  LINES=11 COLS=60 & Color 0E & Title Created By FreeBooter
Echo.
Echo.
Echo.
Echo.       
Echo          Take Ownership Context Menu Enabled   
Echo.       
Echo.
Echo. 

Taskkill /im Explorer.exe /f >Nul

Start Explorer.exe

ping -n 6 localhost >Nul 
Exit


:_RegRestore


Reg.exe delete "HKCR\*\shell\runas" /f > Nul
Reg.exe delete "HKCR\Directory\shell\runas" /f > Nul


Cls & Mode CON  LINES=11 COLS=60 & Color 0E & Title Created By FreeBooter
Echo.
Echo.
Echo.
Echo.       
Echo         Take Ownership Context Menu Disabled    
Echo.       
Echo.
Echo. 

Taskkill /im Explorer.exe /f >Nul

Start Explorer.exe

ping -n 6 localhost >nul 
Exit

I've already taken ownership of the folders, I cannot delete them because they are in use by SYSTEM and another is in use by explorer.exe

How To Delete Files That Won’t Delete - Tech Advisor