You have some confusion about how integers work in python. As the comments above say: python always stores integers in binary form and only converts them to a base when you print them. Depending on how you get x and y and how you need to give back z the code needs to be different
Situation 1: x, y and z are all integers
In this case you only need to do
z = x - y
And you're done.
Situation 2: x, y and z are all strings
In this case you first need to convert the strings into integers with the right base. I think that's your case, since you already deal with int(x, b) which is correct to transform a string into an integer (e.g. int("11", 2) gives 3 (integer represented in base 10). I would advice you to reform your code into something like this:
x_int = int(x, b)
y_int = int(y, b)
z_str = n2b(x_int - y_int, b)
In your code x is first a string and then an integer, which is bad practice. So e.g. use x_int instead of x.
Now it comes down to if your n2b function is correct. It looks good from the distance, although you're not handling signs and bases bigger than 10. There is a broadly accepted convert integer to base b answer so you might take this to be sure.