I cannot look back through history and say what did happen but we can look around and say what may have (and I would argue probably and almost certainly did) happened.
The short answer is that half an eye or 20% of a bacterial flagellum is quite helpful and not useless–as the notion of irreducible complexity would
necessarily imply. For an example an eye without a properly formed lens is better than not having any sight at all (and in the land of the blind…) and a bacterial flagellum without the whip bit (with the omission of 40 of the 50 parts that form it) is in fact the type-3 excretory apparatus.
Videos speaking on these topics are widely available but I recommend
Ken Miller on the bacterial flagellum and
Dan-Eric Nilsson on the eye. You can also refer to
this chart regarding the eye and these two charts (
part 1,
part 2) for the evolution of the flagellum which are taken from
“Evolution in (Brownian) space: a model for the origin of the bacterial flagellum” if you want the heavy hitting scholarly answer to one of your two examples.
I do not simply have ‘chance of the gaps.’ The claim of irreducible complexity is that a system such as the bacterial flagellum or the eye is
useless and
completely worthless when missing any one of its component parts; otherwise it would not be irreducibly complex. Neither of the cases you present meet this burden.
I say this without spite or irony, thank you. I learned new things today answering your question and that makes me happy.