htaccess issues causing link redirects

Okay, something strange is happening.

I have two wordpress installs under one domain name. Everything was working fine until I modified the .htaccess file under the root directory of the main domain. One install is located at domain/home which is the new site I’m working on, and the other is just domain.com for the original install.
I went to make a redirect in cPanel and it wouldn’t allow me to write to the .htaccess file so I decided to change the .htaccess based upon some information I found on the codex page. However, ever since then I’ve had problems with the links on the new site (domain/home) going to the other sites pages. I even made sure that the links on the new site are indeed looking at the new site…

I am running WP 4.0.1 and bulletproof security 5.1.4 on both sites.

How can I “reset” all of my .htaccess files on both sites?

Any ideas?

Thanks,

Brian