Dear Andy,
yes, you have to adjust the vectors accordingly. If it's A1 B1 C1 ... A2 B2 C2 ... A3 B3 C3 ... with a contrast vector [1 0 0 ... 1 0 0 ... 1 0 0 ...], that is the sum across A, then this converts into [1.5 0 0 ... 1.5 0 0 ...] for two sessions. It might be more straightforward if you think of the average, then you would go with 1/3 for three and 1/2 for two sessions. The statistics are identical, but the contrast values are scaled differently. If you want to plot them, then the average ones are typically what you want to show.
By the way, in batch mode there are a few options to adjust the vectors automatically = replicate and/or scale across sessions.
Best,
Helmut
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