Similar things have already happened.
Netwon's laws were rock solid, until we tried to explain really fast or really small things with them. Then we needed Einsteins corrections. Incidentally, we still use Newtons versions for almost everything, because Einstein's corrections are usually a rounding error.
So if we find a huge flaw, we will immediately start using the correction where it matters, and keep using the old flawed stuff where we're sure it doesn't matter.