For practical purposes, the 101-year flood is equal to the 100-year flood is equal to the 99-year flood. We must not forget that the 100-year flood is the flood that has a probability of 0.01 of being equalled or exceeded in one year. However, in most cases we don't have enough records to estimate the 100-year flood within 15% of the real value.
Estimation of the n-year flood is based on fitting a probability distribution to a flood time series. Commonly used and suitable probability distributions are Gumbel, 3-parameter LogNormal, Pearson type III, and others. Naturally, the longer the flood series, the better the estimate, particularly for extreme floods. The distribution is fitted by regression analysis, with the parameters computed by one of several methods, e.g. method of moments. Because of this, we can only talk of an estimate of the n-year flood, and not "the" n-year flood.
We have to remember that the probability distribution is fitted based on a sample, not the entire population. So if we get a flood equal to or greater than our "100-year flood" estimate, our sample has changed with the new data, and we should re-fit the distribution, based on the new sample.
The determination of whether a culvert or drainage system is designed for a particular design flood return period (10-year, 25-year, 100-year) is based on a benefit-cost analysis and/or other economic analysis, including calculation of marginal benefit/cost. The government is trying to optimize the use of resources. In some cases, the 10-year flood is the correct one. In others, the 1000 year storm may be the right one. It is a question of acceptable risk. Fortunately, we engineers in private practice don't have to decide on the level of protection; it's done for us in the policy decisions of the various agencies.
In any case, our duty as engineers is to provide the standard of care required, and to make sure that we compute the flood estimates, the water levels, the flow velocities, the culvert or bridge waterway areas, the channel improvements, the erosion protection, etc using our best efforts and skills. We must make sure that if we don't have the training and experience required, we ask another engineer who does to carry out the work. If we do that, we will be alright in any of the scenarios posted above.