I mean, Polybius might be an example.
But I will say that I couldn’t find explanations for basic DOS commands without the use of an engineering manual from the 1980s. I figured it would be easy to find those online, and while I found the commands, the explanation for how they work and what they can do was basically absent (or at least, written so poorly as to make them unusable).
Again, I consider process more important than product, and consider things like losing source code to be losing that software. You can reverse engineer and emulate it, but byuu (the person who created a cycle accurate emulator for the SNES) will tell you it takes a very long time to do so accurately and may actually be impossible for future software (or even software now), even for games, especially as games as a service becomes more normalized.
Loss of software is tied to some degree to hardware as well, and what you consider loss. Having access to software isn’t really the same as being able to use it - and use is what’s important. Having the binary in the right order isn’t enough (it’s why a lot of preservationists realize magnetic tape, even if it’s the safest medium for digital preservation, isn’t really viable in the long term, since it effectively makes the material completely unusable).
To use a weird metaphor, it would be like transferring a book into binary but then losing the understanding of how binary functions. You may have captured a book, in some sense, but you can’t use it.
(And all of this is a long form way of saying I can’t name specifically a piece of software that is lost in the sense you’re asking for.)