Set up a data compare for a table:
In the 'Map Source Objects to Target, select the appropriate source and target tables and then click on the elipses [...] under the 'Columns Mapped' column
Specify a 'Source Where clause' for the source and target | OK
Run through the rest of the wizard to produce the results
Save the compare project file - File | Save as
Close the 'Data Compare' window
On opening the compare project file again, in the Map Source Objects to Target window, click on the [...] again and the where clauses are not there anymore.
