When I first set up this multisite installation, I set it up so that the main site of the installation was a static page to avoid disturbing our existing site. I did this using a theme containing an index.php which linked to the existing static pages. I've been preparing a new site in the background and now I'm trying to replace the static page with the new WordPress site.
I exported the site I'd been creating, and imported all the pages and posts into the main site. I then changed the theme from the static-page theme to the one I wanted to use. I was expecting that this would make the new site public. However, not only is it still showing the old page, but all the other sites are now giving 404s.
Restoring the .htaccess from backup doesn't seem to help. Reverting the theme doesn't help either. I must have accidentally changed something else, but no idea what! Any suggestions?