This folder is used by the Windows 10 Updater, it contains update logs and files downloaded by the Windows update process.
How to delete the $WINDOWS.~BT folder?
The folder can be deleted e.g. when an upgrade from windows 7 / 8 to Windows 10 failed and you want to free up space on the hard disk. This folder is protected, you can't remove it with the Windows Explorer. Use these steps:
Open a terminal Window in administrator mode and run the command
Source: Microsoft Answers