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I didn't actually find a solution, I ended up using a tree list as a work around. 1 because I couldn't get it to work this way and 2 because it made more sense with my data being hierarchical.
I did manage to get a reply from an Alteryx engineer as below.
"The issue is that we append the ids of all the previous jobs in the chain to a key. In order to keep the instance of the chain going, this key is built out in a cache to preserve all of the proper inputs that led up until this point and we run out of bytes after the 7th app. So, on chained app #8 this error occurs. It does indeed appear to be the same issue for this customer as well as the community post you’ve referenced below.
I have bumped this story up in our back log so the team can take a look and give me an idea of the level of effort to fix this. The fix would be looking at reducing the size of this key so we don’t run into this caching error. If it’s a smaller level of effort to fix, I will request that we look at trying to do this within the current development iteration. I’ll keep you posted on what we determine”
I received this on the 17/05/2017 and I'm yet to hear anything else back