Just like with technical debt, there is a risk of refactoring organizational debt wrong, or over-refactoring. I believe it happened where I once worked. It worked beautifully as a small company, but when the workforce started exceeding 100, the need for better HRM, more formal performance evaluation, better defined reporting hierarchies and career paths became evident. A lot of processes were introduced, but the way it was done induced culture shock in people who had been in the company a long time. I think we lost a few good brains as a result.