DO NOT EDIT CORE!!!!!
Seriously people, stop doing this. Don't suggest it, don't recommend it. If you're not making a patch to fix things, leave it alone.
You don't have to edit the file.
Go in to Network Admin -> Sites -> EDIT the main site.
On that section, click on 'Settings'
Find "Permalink Structure"
Now, bear in mind, if you ever resave Permalinks on your main site, you have to do it again, but this is way safer than editing a file that will be wiped out when you upgrade. Yeah. You lose all your changes when you upgrade if you do what sephil said. Please don't.