Apache2, .htaccess and multisite

Hi, I’m having some redirect problems on my site that I’m trying to sort out, but one thing I realized is that I’m using the Apache2 redirect module, so the plugin is using .htaccess and not the database. But my site is also a multisite network, which means all the sites are using those redirect rules. Isn’t this going to potentially cause conflicts? The rules don’t seem to specify by domain.

If this is a problem, is there any workaround?