Recently I updated to the latest version of Workflow and Pyhtonista, however when I did my jobs that interacted with each other, most of them would not work anymore. All it would say is it can't find the scripts.
A couple would work but the majority would not, what was more strange is if I quit Workflow and loaded Pythonista I could see all my scripts and run them.
This was frustrating, as there were a couple that worked, however thankfully it was a simple easy fix. For some reason as I updated Pythonista, Workflow had gone back to using Pythonista 2 as the default to load the scripts, as nearly all my scripts had gone over to Version 3 this is why it could not find my scripts.
I thought I had removed version 2 from my iPad previously, however after removing version 2 everything was back to normal.
I did try to see if there was a setting in Workflow to pick your version of Pythonista that you want to use, but I could not find one.
I hope this will help you out, it certainly freaked my out initially when all my workflows stopped flowing.
I am always interested in feedback so please feel free to add any comments, or you can mail me here. If you would like to submit a quick tip with full credit and links back to your site then also feel free to contact me.