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The 2019.2.3 build of Prep Builder has a bug in the Aggregation (I spent about a week working with Tableau Tech Support narrowing the problem down to an aggregation I had in my flow and then going through the logs to find the problem). In my case, the logs showed that some of the Grouped Fields were getting unlinked and then couldn't be found when the flow got to the Aggregation (even though they showed up in the Aggregation window). Aside from waiting for 2019.3 to be released (hopefully the fix will be in it), you can do a couple of things: I had to replace my aggregates with custom SQL queries to handle the aggregation on the server side (that might not be an option for you depending on what the data source is you're reading from). You can also try adding a new aggregation branch to the Clean 12 step and then add a new Output to that. If that Output looks good, you should just need to delete the old aggregation and break the flow and then add the new one in it's place. That worked maybe 50% of the time for me but not completely.
Thanks for your considered response!
In terms of using Custom SQL, that won't be possible for this situation since I am specifically using Prep to join a CSV file to my own custom SQL query.
For adding another aggregation branch, I tried that and the result with the bug was the same.