Which "underlying datasets" are you contemplating removing from the application server?
If they are the datasets that are used as inputs to your models (source data that is pointed to by a Data Source/Input Dataset node), all of the nodes will remain in your diagram(s), as will the results. If you want to re-run your analyses at another time, simple restore the source data sets.
If, however, you mean the data sets that are part of the Enterprise Miner projects themselves, the nodes will remain in your diagram, but depending on what's deleted, the diagram(s) may no longer run and may no longer have results, and could even become corrupt.
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