Update drupal module with existing custom changes
You are not supposed to hack modules or core directly, because when you update drupal and modules your changes will get lost.  If you have some valuable changes or corrections that others might benefit from its best to submit a patch to the issue queue of the module and if maintainer accepts them you benefit as well.

If maintainer does not decide to use your changes you can also consider making your own module or perhaps with a custom theme you can  accomplish what you want to do.  Drupal has a great system in place to override parts of code with your own logic without hacking core or contributed modules.

If you actually decide to keep those changes as hacks you will have to do your own merge confict resolution as drupal internal update process or even drush updating will not do it for you.