When the reference run is performed, the tool will partition out the design as it is performing synthesis. Then, when the incremental run is started, it compares the elaborated design with the reference run and identifies the changed modules. The partitioning from the reference run is initialized in the incremental run. The partitions that contain the changed modules and the partitions that are affected by them are marked. Based on this, the tool will perform synthesis on the partitions that have been marked. The information on how much of the design and what parts of the design were re-synthesized can be found in the log file after the incremental run.
This information will be in the “Incremental Synthesis Report Summary”. The following is an example of the report.
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X-Ref Target - Figure 1-17 
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This section will have information on which sections of the design changed and needed to be re-synthesized. In addition, it will also have information on how much of the design changed from reference run to incremental run.