You need to change $CFG->wwwroot to reflect the new Moodle URL. That's it. I'm assuming you know what you are doing with the DNS and web server changes.
You should also run the Search_and_replace_tool to update any links in the Moodle data.
What you can't do is have Moodle work with two different hostnames (.net and .com in your case). What you could do is simply redirect any .net to .com in your web server configuration).