There may be a better way to do this, but this is what I did, and now the Caffeinate Control workflow works for me.
I tried to make a step-by-step guide for you. Hope it helps!
Step 1
Open up Alfred Preferences and go to the Workflows tab
In your list of workflows, right click "Caffeinate Control" and do Open in Finder, like this:
Step 2
Now you should have a Finder window open to the Caffeinate Control workflow directory, like this:
I have highlighted the 2 files you will be editing: conf-and-help.scpt and library.sh
Step 3
Open conf-and-help.scpt, which will launch the Script Editor
Search for "Alfred", and you will find this line:
Yours will say Alfred 2, so change it to Alfred 3 like in mine
Save the script and quit the Script Editor
Step 4
Open library.sh in a text editor (I used Sublime Text, but TextEdit or any other text editor is fine)
Search for "Alfred", and you will find these 2 lines:
Yours will say Alfred-2 and Alfred 2, so change them to Alfred-3 and Alfred 3 like in mine
Save the file and quit your text editor
That's it! Now the Caffeinate Control workflow should be working again
(Note: after completing these steps, you might have to quit Alfred and then restart Alfred, but I'm not sure if that's necessary - I can't remember if I had to do that or not, but if it's still not working for you, then try that.)