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Not sure which script you are talking about. If any of the Inquisit IAT scripts, there is no need to change anything or re-calculate manually. D is a difference score, essentially calculated as
(mean latency in "incompatible" blocks - mean latency in "compatible" blocks) / standard deviation
The group merely determines whether a given participant completes the "compatible" or the "incompatible" blocks first. This has no effect whatsoever on the D-score as the Inquisit script's calculate them.
For completeness sake, the "lines" that determines the group assignments are the /subjects and /groupassignment attributes in the <expt> elements.
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