The navbar template contains more than just the navigational links. If you wipe it completely out you're also removing the Notice condition and more; like the Ad Location call for the ad_navbar_below template for example.
You'll need to use some basic coding search skills to see where what you want to remove begins and where it ends. For example if you just want to take off the bar below the breadcrumb navigation and login/member box, you would look at the template code and find:
Code:
<!-- nav buttons bar -->
then search down and find:
Code:
<!-- / nav buttons bar -->
..and snip out everything between.
I would recommend reverting your navbar template back to default. Copy the code to Notepad so you can have a better view of the whole template, snip out carefully what you don't want, and paste in what's left into the template in the AdminCP page and Save.
[high]* Theater takes the twitchy bunny and flees...[/high]