When WordPress updates core, it doesn't overwrite the
/wp-content directory. But if you're updating the plugin, you'll overwrite your plugin directory with new files.
Rather than adding a file manually to the plugins directory, I'd recommend using one of two approaches:
Host an Alternative Repository
I'll let you Google how to do this, since there are a few good tutorials on it already, and at least one outstanding book. But you can host your own separate repository for the pro version of your plugin. Push out updates directly through that and you'll control the update process 100%.
Offer a Companion Plugin
key.php file as a separate plugin that users drop into the
/wp-content directory on its own. Then they can activate the regular plugin and the "pro" plugin separately. When they update the regular plugin, nothing will happen to the "pro" files since they're separate.
Just make it so the "pro" plugin requires the standard one be activated.