Well, I can tell you I've used it for...probably 6 months now...with no issues, beyond that it can sometimes take a minute or two to go through the process. And that's not really a problem so much as it's me being impatient.
I should add that I also have many custom ringtones, and this has never had any affect on those. My understanding of the app is that it's updating the index, not changing the locations of files or anything of that nature.
Atrix 2: Rooted, not yet ROM'd.