[taeric]

This is true of any image based development, as well. You can get the same thing in Java with hotswapping code, even.

That is to say, this is a bit of a concern, but isn't typically as large of one as you'd think. There are plenty of ways to make it so that you can't reason about a program. In general, you avoid doing those things.

Specifically to your question, I think, the biggest trick is that you rarely use the REPL as where you type your code. For that, you typically still use files and eval the file into the environment controlled by a repl. Even in emacs, you rarely just execute elisp from the scratch buffer. Unless you know it is something you don't care to keep, of course. Instead, you are working with files and evaluate the file on a regular basis.