Hello! 

There is no link or connection between these two streams.if you are willing to work in aviation fields you can work but MS in aviation is not possible i guess because Ms is master in science which is a continuation to computer science.

One of my friend stopped his b.tech and joined in aviation courses. If you are very much interested you can start over but it is too risky in short life.this is  a tough decision at this point of time so better to choose ms in case and be on safe side.