Dear Andy,
I would suggest you set up a contrast manager batch and redo all contrasts (at least for the subjects which do not have the desired contrast order). If these are only a few subjects, I'd run this through the batch GUI. If you want to redo all subjects, you should have a look at the "Save batch and script" option to enter the path to all SPM.mat files with a bit of MATLAB code.
Hope this helps,
Volkmar
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