As someone who has worked on the tech side of sites powered entirely by organic SEO, I've definitely seen the same penalties occur when cosmetically "cleaning up" URLs or code.

In the author's case, they moved to sub domain for easier maintenance. The article ended with a transparent way of keeping the old URLs and correctly improving the tech behind the scenes.

Be careful of changes, even if endorsed by Google, when things are working. More often than not, there'll be a mistake, you send the wrong signal to Google, and you take a hit. Only do it, IMO, when there's nowhere to go but up :)