Hi,
I have been playing around with this scenario.. I happened to have two spare SSDs with Windows 10 UEFI on them.. I had been running Legacy at the time of my reply..
Making a long story short.. I never ended up with two WindowsBootManagers..
I ended up with two "Microsoft Windows" options.. After selecting one of them, I ended up with a Microsoft Windows and a WindowsBootManager.. The second Microsoft Windows selection never converted, but was bootable selecting the "Microsoft Windows"..
I then used a 3rd party bootable tool called Parted Magic_2019_11_04... It has a File Manager that I used to RENAME the "EFI" and "Windows" folders in the "EFI" partition rather than deleting them.. This solved the problem of which drive got booted into, but I was still left with a "Microsoft Windows" boot selection... It didn't work, but was still on the list...
Out of curiosity I then deleted the actual "EFI" partition.. Problem solved.. The unwanted SSD does not appear on the Boot Options and the machine does not try to boot to it.. All files on the drive are available..
In your case, you will need a 3rd party tool to delete everything on the HDD, or to edit it.. Any of the Parted Magic versions prior to the one I mentioned should work.. I mention this because the earlier version were free and could be downloaded as a bootable ISO.. That is no longer the case..
One other possibility... Use Windows 10 installation media and start out doing a Custom Install with your M.2 drive removed or Disabled in Bios.. You can delete everything on the HDD this way..
Just stop the installation after the deletions... Boot to your M.2, and use Disk management to reformat the HDD as you wish..
Any other questions, feel free to ask..