Sorry for the response delay...
You can write a Matlab script to edit the file structures manually.
You need to rearrange the indices of the following matrices: TF, RefRowNames, RowNames, Atlas.Scouts.
If the TF matrix is symmetrical and compressed, you need to unpack it first, reorder both rows and columns, and repack it again, as explained here:
How the Corr matix is saved?
For getting started with Brainstorm scripting:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting
Please let me know if you need additional details.