Thanking supervisor after a year
There are only two possible options here.


Do nothing. Most probably, the professor never realized that you did not thank him for his supervision. He provided what was probably a good reference letter and you already thanked him after getting a job, so I suspect he does not have a bad opinion of you.
Clear up your mind by sending a polite email stating that you just realized you might not have thanked him for his participation in your master project. I do not think this would be awkward. I think any supervisor would be happy to receive such a message. 


Both options are good.