Question regarding .htacess and Permalinks

I currently have Permalinks enabled on my blog. On my .htaccess file I also have some custom lines I have typed out.

What I need to know is, if I update the Permalinks structure will WordPress remove my custom lines, or will it just edit the WordPress section?

Oh, and my custom lines in my .htaccess aren’t between the ‘# BEGIN WordPress’ and ‘# END WordPress’ space; they’re right above the ‘# BEGIN WordPress’