If it is VP of Engineering and he/she is reporting to you, one option would be to delegate the responsibility to manage the senior SWE to the VP and make both

If it is VP of Engineering and he/she is reporting to you, one option would be to delegate the responsibility to manage the senior SWE to the VP and make both accountable to deliver the results. I think you also might need to reconsider your position as a CTO, if a VP could simply bypass you like that you have bigger issues at hand than managing the protege.