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I have a simple works flow that starts with a Run command tool which runs an exe file that connects to a web server and generates the results in a CSV file, then in the workflow I have formula tool that adds a new timestamp field in addition to the existing three fields in the CSV file, and the last tool in the workflow is an output data tool that appends the data (Delete Data and append) to a SQL Server table.
In configuration of Output data tool and in Append field map section you can use custom map option to manually map the fields. The issue is when you complete the custom mapping and save work flow the next time you open custom map, you don’t seem the mapping and in fact custom mapping option is grayed out, it seems you haven't lost the custom mapping but for some reason the option is grayed out, and you cannot edit it(make any chanages). Only when you run the workflow the custom mapping is back and visible.
I'm using V10.6 and 11 beta2 and cannot reproduce the behaviour you mention on my installation of Alteryx.
I don't know if this affects the behaviour, but can you check within the yxmd xml file, the <AppendMap> tag? Is <AppendMapping mode="Custom"> and then all the fields with the corresponding with Source and Dest correct?