@drdave79 I've been using Retropie for over 5 years now. Every experience I've had with updating Retroarch has had it's downfalls, it's never a smooth transition because it effects so many systems attached to it. I agree with leaving a running system as it is, but after so many new versions are released you loose a lot of performance options.
So it's always up to you, but I go by a basic rule of thumb....I wait till enough new versions have been released to make it worth the trouble I know it's about to cause. Backup what you have and be ready to pull out some hair (or stubs in my case).