A few interesting things I've found trying to google this
-CBS did released a press release earlier this year (4/3/12) that they reached a agreement on an extension with Worldwide Pants, Letterman's production company, & the production company that is obviously behind Late Show, & Late Late Show. In the press release they state the extension carries through until 2014.
-According to Louis IMDb page, he was a writer on Late Show w/ Letterman in 1995, for 11 episodes.
-Louis has appeared on Letterman 6 times, the most recent was in 2011, when he appeared as a "guest-comedian".
I really haven't found anything that would suggest that there is an heat between the two, but then again Letterman did sign an extension with CBS in 2012, & Louie has not appeared on Late Show in 2012 at all, so maybe there is some truth to it, though on the other hand if there was, wouldn't CBS be able to sue FX and/or Louie for defamation of character or some shit? They do do a really good job of making Letterman look like a real asshole in finale. My guess is that next season we see more of this relationship play out.