Chaining transformations provide an extra degree of flexibility and power to transformations. For example, you might have a situation where two transformations have a common element. This can be separated out into one transformation, and then the original transformations can be transformed from the common point. The separated transform could even produce a useful model itself.
Enterprise Architect provides for chaining transformations, by enabling transformations that have already been performed on target Classes to be performed automatically next time that Class is transformed to. To enable this, select the Perform Transformations on result checkbox in the Model Transformation dialog.