Since the window already exists and has a default size, it must be registered under a specific mode in the filesystem.

Find the file defining the size, i.e., the "wsmode" file that defines the mode under which it is registered, and change it. Then register the changed mode under the same name as the original mode in the layer. If you want to make sure that yours overrides the default, set a dependency in your module on the module that defines the original mode.

Generally it is better to create a whole new mode, since you then will never have a conflict between two different definitions.