The Sunna added other licenses, but did not take away the license of in 4:101. You can call that many things, but abrogation is not one of them.
What it is called in the jurisprudence books is خاص أريد به العموم (a specificity meant for generality). What they mean by that is that the specificity is meant as an example contingency, not as the sole contingency. Thus, we are allowed to shorten the prayer whenever there is a good reason to do so, e.g., fear of enemy attack, exhausting travel, etc.
In a similar light, one can understand the hadeeth where the Prophet (PBUH) has advised that one may make up for a missed prayer, because he overslept or forgot, by praying it when he wakes up or remembers. These are two example contingencies, IMHO, for making up for missed prayers. They are not an exhaustive list. Those who get that, such as the late Sheikh Shaarawi, may God bless his soul, have ruled that missed prayers, for any reason - including deliberate neglect, may be made up for later. Those who don't understand it that way, have ruled that there is no way to make up for missed prayers!