VFDs have come a very long way since then. They're smaller, cheaper, widely used, and far more reliable. So cheap and reliable that the cost of (2) VFDs is pretty close to that of a VFD with a bypass. The size difference is minimal as well.
If your primary VFD fails, would it not be more beneficial to have a redundant VFD that will modulate and operate your equipment the way it was designed? Or would you rather put it into bypass, where the motors run at 100%, guzzle energy, and could blow out duct work in an air-side system?
Yup, I'd go with the redundant VFD too.
You can use two separate VFDs or you can have the two VFDs enclosed in a single cabinet for easy installation and identification.
Yaskawa offers this as a factory provided package readily available to the engineering community.
So get rid of those bypasses along with your Beta Max video player and upgrade your system for full redundant functionality.