I believe that the closest analogues to your physical examples arise when mathematical texts are, at the time they are written, regarded as being precise, but are later regarded as being insufficiently precise or rigorous, so that the nouns in the older text are seen as requiring reformulation in "modern, rigorous terms" before they are accepted as directly and unambiguously referring to some mathematical entity.

For example, near the beginning of Euclid's *Elements* we read, "A surface is that which has length and breadth only." Today, many mathematicians would instinctively react, "Say what?" Before they can make sense of Euclid's definition of a surface, they need to reformulate it in modern language. Now, once they do so, they will deny that Euclid's surfaces have "disappeared," because according to the standard platonistic philosophy that forms the basis of the working mathematician's conception of the world, the universe of mathematical objects is an eternally existing thing, and it is impermissible to declare that objects in that universe cease to exist. Rather, we say instead that Euclid used *language* in an old-fashioned manner, and that we need to translate his text into modern language before we can reliably determine the referents of his nouns. Once the referent of the noun is established, then it lives forever and cannot disappear; the only things that can "disappear" are *ways of speaking* that are later judged to be not clear enough to unambiguously describe eternally existing realities in the mathematical universe.

If, however, one takes a less platonistic view of mathematics, then one might simply say that Euclid's surfaces (and other concepts) in their original form have disappeared, but that the *essential mathematical content* of the Euclidean theory has been preserved. In fact, if the modern reformulation is done carefully, much of the older text can be preserved verbatim. There will, however, be some instances where the older terminology and sentences lack a one-to-one correspondence with the modern version; older concepts that are judged to be superfluous or vague are just dropped. In this sense some things "disappear," and it's not just that certain *words* have fallen into disuse, but the *concepts* that they were supposed to refer to are deemed insufficiently precise or rigorous.

As others have mentioned, infinitesimals are another example of this kind of "disappearance." In mathematics proper (as opposed to science and engineering), infinitesimals as they were conceived in classical calculus *no longer exist* in mathematics, in the sense that the concept that people used to have is no longer considered to be rigorous or precise enough. Obviously, the *essential mathematical content* has been preserved in modern treatments (whether "standard" or "nonstandard" analysis), and some theorems can be preserved verbatim when the words are suitably redefined. But there has been a definite shift in the underlying concepts, even though "no matter has been created or destroyed" in the platonistic universe of all mathematical objects.

A similar story can be told in other cases where there has been a change in "rigor." Algebraic geometry may be another example where so-called classical Italian algebraic geometry was later regarded by some as lacking in rigor.