Issues like this are why I write everything into scripts and pipelines, even the munging. This way everything is documented: the environment, the input, the output, the log file, what ran, and longform comments with why I was doing it.
Good choice but that for me breaks the "carpe Diem" part of the inspiration that can go away in a whim, that it's what I have when I'm writing (complex) one liners in the shell.
Just have two windows open, your console and your editor. If you ran a command that worked just copy and paste it into the editor. There's your script if you didn't want to get fancy. If you copied your initial cd command or whatever you'd know what the relative paths were referring too as well (although this issue is why I have gotten into the habit of using a path variable instead of relative or anything hardcoded).
