DOS Quake has issues with saving, so I am doing this test in GLQuake. That should be fine as QuakeSpasm was based on it. I also play in Nightmare.
I launched the game and saved immediately. I then exited and reloaded. I then reloaded once more. I killed the Fiend and reloaded. I died to the Fiend and reloaded.
Do you use Quicksaves and Quickloads? That might be a variable worth knowing. I am loading through the menus.
I wandered around every area besides the Water that I could and took about 15 minutes to do such. This should provide a reasonable amount of time for something to occur.
All nine were still there, no issues whatsoever. Did you go to the Water earlier and leave the Rotfish alive? Were they alerted in any way? My test left them alone for those minutes so that if something happened while they were idle, it would occur.