The boot sector is a region of your hard disk that contains information that is used to load your operating system. If you delete boot manager, you will not be able to boot to the desktop.
In case anyone else sees this: this is *NOT* the answer, despite coming from Microsoft Support.
The question is about the object bootmgr in C:$Windows.~BT\NewOS.
This is not the boot sector of the hard drive. That is outside the file system, and not visible to Explorer. Nor is it the active bootmgr that is booted by the boot sector. That is in the root of C:, not in any sub-directory.
The object in c:$Windows.~BT\NewOS is AFAICS a symbolic link that may be invalid. Disk Clean-up (Remove Windows Installation files) may remove it, but as most of $Windows.~BT has already been deleted in this case it may not work. In which case it is probably stuck there until the disk is reformatted. Annoying but not really a problem.