Most people actually working on Matrix have been aware of state resets for quite a while. Hydra is just the name of the project which addresses them. There are 3 phases, of which the 1st covers the most serious ones; the 2nd and 3rd phases should drop next year.
As an analogy, it's not dissimilar to how Git has added various different merge resolution approaches over the years in order to come up with more predictable and more "do what i mean" algorithms (resolve, recursive, ORT, octopus, etc). It's slightly different in that a bad merge in Matrix feels very unexpected and problematic, whereas manually unpicking collisions in a VCS is just part of the territory.
Before project hydra people didn't know about the room exploit either. They just knew that rooms exploded somehow every once in a while.