You've come to the right place for help, I know how you can change an employee to a contractor.
You may need to enter the employee again to be a contractor and enter a unique identifier such as a syllable or character to make it slightly different. This is to prevent entering the same name when adding an employee as a contractor.
You can also change the name of the employee to a different one. Then, enter the real one with a middle name for the contractor.
I'd also recommend recreating their contractor profile in QBO. You can then re-enter contractor payments as either checks or bill payments if necessary.