The upgrade was fast and easy, definitely not something I expected and I had backed up my machine to do an install from scratch, but not required at all.
Just re-installed them, all is well again.
And, "no matter which OS" is definitely incorrect. I've done an in-place upgrade of an OpenBSD system for the better part of six years (twelve upgrades, twice a year). The _recommended_ approach on that platform is to do _in place_ - not clean install. It's how you maintain library compatibility with all your legacy apps.
With that said, there are fewer things that can automatically go wrong in any clean install (as opposed to the things that can go wrong manually with a clean install, like forgetting to deactivate Adobe CS, or that scripts accustomed to sshing in to your server don't take kindly to unannounced host key changes).