Yeah, I ran into the same issue. I had to make all my changes again after losing them the first time.    When clicking Finish after making the Python changes, it resets those scripts to defaults, based on the inputs in the add-on builder.  You need to setup any other inputs that you need configured in the add-on Builder, then add the fields and code to those Python scripts.  Might be best to keep a backup of them with the changes applied, in case you need to do anything else in the add-on builder in future and you accidentally overwrite them again. 
						
					
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