The version number is what is on the main stylesheet as that is where WP is pulling it from and the theme itself may or may not have built-in code that checks the version against a remote server to know if there are updated versions of your theme. As I said, every theme is different.
But I am failing to see how this is relevant to your issue of custom changes. Because regardless of any version, as long as it is an update from yours, you would still need to port over your custom changes.