I needed to set a cookie via .htaccess, to ensure it was always in the browser, regardless of what the website was doing. Setting a cookie is rather easy, it will look similar to:
Header set Set-Cookie "cookieName=value; Expires=Wed, 15 May 2222 07:28:00 GMT"
The next morning I attempted to login to the site and could not. It turned out the login cookies were not being set. The issue was insidious. Re-read the line above, at first glance it seems fine when you want to set a cookie, however if there are other cookies that need to run you need to add the cookie.
This three letter change resolved the issue and allows all the other cookies to operate properly:
Header add Set-Cookie "siglock=hello-world; Expires=Wed, 15 May 2222 07:28:00 GMT"