James,
I've done what I believe is correct, which is exactly what you've done. The script executes in terminal but when it says it is running in ekos it does not do what it is supposed to do. I'm going to suggest that there is something I don't know about how Ekos executes shutdown scripts. I used to use scripts all of the time to move images from the default directories to the proper directories in between each capture and that worked perfectly.
Dave

Thanks for checking and glad to hear it's not just me. I was getting to all kinds of crazy python code when I saw your message!

So unfortunately I can't execute a shutdown script, are there any other options to make the pi shutdown at a fixed time do you know?

I always have a VNC open and manually shut the Pi down with sudo shutdown -h now, which I assume works because the Pi goes away. I would test it on my Pi, but the Pi is outside and the ambient temp is 115F. I'l have to wait until it cools off a little before I go out and power it up. I will later. I have to know.

I think I figured it out.Works in the scheduler as a shutdown script. When bash closes, it gives a return code.

Of course you don't want to kill indiserver - I just used that so I could see it working.

Hi, this will be an unattended observatory so a manual shutdown is a no go

The killall approach will happily kill indiserver, how do I translate that to shut down though?

So, after downloading the EKOS source code and getting to the point where the QT process launches for shutdown I finally managed to figure it out, I was simply missing #!/bin/bash from the start of the script, this works:

#!/bin/bash
shutdown now
exit 0
 

I did mention a lot of posts ago when I gave you my examples that you needed that, it’s not a script without it…I said it had to be a bash script and you said you had done that…?? could have saved yourself a bit of time there….

When I asked explicitly "Does it care about any headers or file extensions or should it literally just contain that one line?" I needed "No, it has to have a header"

All the examples were just one liners but it needs to be a defined script at the top (not necessarily bash I might add), I'm getting there now though but thanks for chipping in

This was my example….from earlier not a 1 liner…its not a script without the bin/bash, I also posted that too….
but never mind you have sorted it now….

Have you tried 
#!/bin/bash
sudo systemctl poweroff