Unable to boot into cloned drive after formatting old drive

The problem was with my EFI partition.

As Fleet Command mentioned, cloning the hard drive was not enough. I attempted to mark the system partition as active, but that didn't help either since my new hard drive was originally partitioned as GPT, not MBR.

To fix the issue I used BillyGun's answer from here: https://answers.microsoft.com/en-us/windows/forum/windows_10-performance/windows-10-bootrec-fixboot-access-is-denied/747c4180-7ff3-4bc2-b6cc-81e572d546df

Windows 10 Installation Media:

1. Insert the Media (DVD/USB) in your PC and restart.

2. Boot from the media.

3. Select Repair Your Computer.

4. Select Troubleshoot.

5. Choose Command Prompt from the menu:

Type in the command:

Diskpart

Type in the command:

List disk

(Note which disk is your Boot drive number mine is 0)

Type in the command:

Sel disk 0

Type in the command:

List vol

(Note which volume is the EFI partition mine is 4)

Type in the command:

Sel vol 4

Type in the command:

assign letter=V:

Type in the command:

Exit

Type in the command:

V:

After you have assigned a drive letter Using Diskpart You can format the EFI partition:

Example: if you assigned a letter V to the partition the command would be:

format V: /FS:FAT32

After the format you need to recreate the EFI directory structure with the command:

MD \EFI\Microsoft\Boot

Then change to the Boot directory with:

cd /d V:\EFI\Microsoft\Boot\

Then run:

bootrec /FixBoot

Finally run:

bcdboot c:\Windows /l en-us /s V: /f All

Type in the command:

bcdboot C:\windows /s V: /f UEFI

(This replaces the above crossed out lines and works in Win 10 1709)

I actually ended up skipping formatting and recreating the EFI structure since I had the partition there already.

Cloning a hard disk alone isn't enough; you must mark the new System partition as active and then reconcile the boot configuration data (BCD). In BCD, the address of the partition from which to boot is given in the form of the SSD's unique ID, plus partition ID. If you don't reconcile, the boot loader will still look for the old hard disk.

Just for the record, the reconciling can be done by a utility called "Bootice". But you are well past that stage. Try this:

1. Procure a USB flash drive with Windows Setup flashed into it. Microsoft Media Creator will help you build one, using another computer.
2. Plug it in and boot from it.
3. Confirm your language, locale and keyboard layout and click on "Next".
4. Choose "Repair your computer" from the bottom left.
5. Choose "Troubleshoot".
6. Choose "Startup repair".
7. Wait for the startup repair to complete.

If it didn't help, then I am afraid solving your problem is going to need you providing additional info.