Hi Aleksander,
My name is Igor, it's a pleasure for me to help others and I'll do all my best to help you.After drive cloning both old and new drives have identical identifiers so system cannot distinguish them sometimes. Partition deleting does not remove drive identifier, one need to clean the drive or change the identifier manually. Seems your partition manipulations confused the system.
Please use Windows installation media and try to repair your system boot.
How do i change the drive identifier manually?