How do I clean windows off an old drive but leave the rest of the files on it?

I'm currently in the process of moving from an HDD to an SSD.

I have moved my windows install from my old drive to my new drive using the windows media creation tool and a usb drive.

Currently I have windows booting on the new drive and old drive is not plugged in at all. Last time I tried to boot at this stage with both drives plugged in, something royally went wrong.

Is there a way I can clean windows off the HDD so I can boot with both drives plugged in?