I am trying to assemble several datasets into one. I need to add the edited or added data in to our original/master/parent/production data set. I also need to delete the data that should be deleted. I have a separate feature class for the added, edited and deleted data. I am not sure how to delete data from the original geodatabase. I think that I am getting two ids for the added and edited when they are added to the output/published geodatabase.
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This article will explain how to do it with ArcSDE - I guess it a similar logic with GDB:
http://fmepedia.safe.com/articles/Samples_and_Demos/Updating-Inserting-and-Deleting-features-in-an-unversioned-Geodatabase