Update to newest WP broke .htaccess

I have a client site that was completed and handed off, but I got a contact from them today that the site had broken.

Main URL is http://www.thediversitycoach.com.

On logging in and poking around, I believe what’s happened is that WP was updated to the newest version and the .htaccess was overwritten, clearing out the DirectoryIndex calls I need to make the site work. I’ve fixed the main site (with DirectoryIndex index.php/home/), but the problem is that it was a multisite installation with subdirectories, and the subdirectories are pretty much inoperable.

One subdirectory, /bloglanding, had a masked redirect so that people who went to http://www.jamesorodgers.com, the address for his blog, would see the content at thediversitycoach.com/bloglanding. From there, they could click different links to go to the content at thediversitycoach.com/jamesorodgers, the second subdirectory.

The masked redirect used this method: http://webstarthelp.com/forwards.html

Right now, I can’t even access the admin panel for either subdirectory, let alone any of the content. If you visit jamesorodgers.com, you see part of the content for the page, but it loads without formatting and without pulling in the theme, other images, etc.

The problem is, I can’t figure out either A)how to tell the site to go to the subdirectory’s files when at jamesorodgers.com, or B)if I need a separate .htaccess, where to put it, since it’s subdirectories and not subdomains. When originally done, I had to livechat with tech support at HostGator, his host, and they actually made the changes for me, so I don’t remember what was written – but when I tried that this time, the tech said it was outside their scope of support to do that. (Figures).

Any help? Let me know if there’s any more information I can provide..!