System Partition and Boot Partition on Different Drives

I have Windows installed on an SSD, but as shown, the system drive is the HDD.

This happened after I dual-booted windows and linux (with linux being on a partition on the HDD) and then removed the linux partition all together. This resulted to an inability to boot into windows, so I used easyBCD to add it to the boot list and get selected automatically. This results in a slow booting and various bugs around the system.

Many software that allow OS migration detects the HDD as the OS drive, and so does the mbr2gpt /convert /allowFullOS command in CMD.

Is there a way to resolve this without formatting / reinstalling ?

Disk Management

CMD

Solution 1:

It seems you are running a MBR system.
In that case it is relatively simple.
If you remove the HDD you basically have a single disk Windows with a broken bootloader.

First make a bootable Windows install media (USB or DVD). You can use the Microsoft MediaCreator tool for this. Select the same Windows version as you are currently running. (Warrning: Microsoft always offers the very latest by default. This may be newer than your version.)
Then disconnect the HDD. Obviously your system won't boot from disk anymore, so boot it from the install media.
Go into the recovery mode and let it repair the boot problem.
This should setup a fresh bootloader on the SSD.
After that you can re-attach the HDD. Make sure in the BIOS you remove the HDD from the list of bootable devices or your computer may still try to boot via the wrong bootloader.

Do all that and make sure the system is running fine BEFORE you try to mess with mbr2gpt and a conversion to UEFI boot.
(I'm guessing that is your eventual goal, otherwise the GPT conversion would be pointless.)

Solution 2:

Solved:

I ran "easyBCD" and changed the boot drive, that had the bootloader rewritten into C drive.

I then used "minitool partition wizard" to set the HDD drive to Inactive.

I then used the command mbr2gpt /convert /allowFullOS to convert the OS drive to GPT and enabled UEFI support, Finally it boots quicker and cleaner.

This is how everything looks now: