This is now implemented. If you include a REFERENCE_REFLECTION_FILE in a CRYSTAL block it will be used for determining the setting and assigning the spacegroup. This should contain a single data set with intensity values. Currently the free set is not copied from this - I will write a small "jiffy" application to copy the FreeR_flag column from your existing data to the newly reduced data, as it is unusual to include the Free column in intensity data.
0.2.6.1 is currently undergoing testing.
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