Your guess is a good one, that something to do with the cloning process caused GPT attributes to clear, GUID type codes maybe to muss &/or partition positions to scramble. Then Windows wouldn't boot. You may have done stuff at the BIOS boot menu &/or BIOS/Windows did it automatically to end up with an abnormal BCD that does at least achieve a boot. But it looks like the Frankenstein monster to me. And I'm unsure it will function well in all circumstances.
That's right. Once you've got an external recovery environment, go ahead & do that code I wrote. You will have the means to undo it, if necessary, even if you can't get into the internal recovery environment (your Recovery partition). Shift+Restart will most likely return to Windows if there is no access to the internal recovery environment. But once I saw it go to a useless dwarf version (it had no Troubleshoot button, IIRC). Then, "Continue" did get back to Windows.
Here are the alternatives for an external recovery environment...
(1) For the Repair Disc...
(a) Type "Control" into Search, & click "Control Panel".
(b) Click "Backup & Restore (Win 7)".
(c) Click "Create a system repair disc" to make the DVD.
Warning: The last few times I tried, it just chewed up the DVD & made it unusable.
(2) For the Recovery Drive, type "Recovery" into Search, & click "Recovery Drive". You need at least an 8 GB USB drive. This is a better option. Not only does it provide a recovery environment, but it can do a reinstall of the same version of Windows that existed when the drive was made.
(3) For Win 10 Installation media...
https://www.microsoft.com/en-us/software-download/windows10
Download Windows 10 - This is the latest finalized Win 10 version, currently 21H1.
Download MediaCreationTool21H1.exe & run it to make a Windows 10 Installation USB drive or burn an .iso to DVD. Follow the instructions under "Using the tool to create installation media". As it says, match it to the Language, & Architecture(x64/64-bit or x86/32-bit) of the computer on which it will be used. The Windows Editionto take is "Windows 10", which includes both Home & Pro. This can do a clean install or a repair-install, & it also has an external recovery environment.
(4) Here is how to boot them...
You need to press an F-key during boot to get to the BIOS Boot Menu. If you don't know it...
https://www.sysnative.com/forums/threads/get-access-to-bios-settings-boot-menu-f-keys-hotkeys-by-system-manufacturer-oem.23010/
Get access to BIOS settings & Boot Menu: F-keys/Hotkeys by System Manufacturer (OEM)
Note: That is an informative 3rd-party site. But I know nothing (bad or good) of any downloads or links that are there.
(a) Insert the DVD or plug in the USB Installation media.
(b) Bootor reboot the computer.
(c) Press & hold the F-key at the manufacturer's logo (or at the black screen just before the logo).
If the key was pressed in time, mine shows activity at the bottom of the screen,
& the BIOS Boot menu soon shows up.
(d) From the BIOS Boot Menu, choose the "UEFI" option for the media, if offered.
Mine names the device brand & precedes it with "UEFI:".
(e) If it were a DVD inserted, you get a message to "Press any key" to boot it.
If not pressed in time, the DVD will be bypassed & Windows will try to boot.
(f) When the Installation media boots, select "Repair your computer" instead of to install.
The computer will reboot to the Recovery Environment at the "Choose an Option" screen.