When I call out a window contractor to fix my window will he replace window glass or the entire window?

Most contractors will replace the entire window. If they were to simply replace the pane of glass, while it would be vastly cheaper, the finished job would not last as long and could cause damage to the contractor's reputation in the long run. By replacing an entire window, the contractor is able to verify with their own work that the job is done right (assuming the window is quality). 

Another reason is that many replacement window companies offer warranties on their products. If the contractor were to simply replace the pane and re-seal it, they would have to provide a warranty in-house. Most contractors are unable to offer such service packages, whereas a window manufacturer almost certainly will.

Essentially, it is safer for the contractor in terms of customer satisfaction and dispute resolution to simply replace the whole window and make sure the job is done professionally.