In 2.0.1, whenever a workflow was exported, all the custom functions were exported. However, in 2.1, this behavior was changed to export only those functions that are referred from within the workflow.
Hence, now whenever a workflow is exported, only the used functions are exported.
Example: A function will get exported if it is used in defining a value for an attribute within the workflow.
That sounds like a better solution but then there is still an issue in the WFA version I'm running since one of my workflow uses 2 functions and when exported only one of them was included.
I noticed this when I decided to start from scratch with my WFA install. I exported my 3 workflows, reinstalled WFA, imported the workflows and 2 functions were missing. I rewrote them because they were pretty simple and I had done a backup before reinstall but still...