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You would automate this process via the Batch Loader built into FDM. The process for using this is exactly the same wheteher you have one or multiple target applications. The ultimate target application is driven by the location name embedded in the BatchLoad file naming convention. Each of your different target adapters will be associated with one or more locations in your FDM Location metadata setup.
Do you have 1 load file that you want to load to 6 different target applications? Or 6 load files, one for each application?