Quantum computers will under the surface store and arrange data differently. This will definitely affect "machine language" the layer of software that communicates directly with the hardware, such as the code that underlies an OS like Windows or Linux, or the result of compiling a language such as C++.
But most application software developers don't write machine language. As an application software developer, these changes will probably be abstracted from you meaning you will never have to deal with the, unless you decide to become an OS programmer.
You will still program in C++ or C# or Java or any other language and the new compilers will compile the software to run on the new quantum OS. The people who write the OS or the Compiler will have to deal with the differences, but in all probability you will not.
The only thing I can think of that might change is that languages such as Java or C# may begin to include new optional data types that you could not have without quantum computing, but That's just a guess, I might be wrong.