Hi Tom,
Note that it might be more meaningful to concatenate your epochs in time first before computing the coherence in order to get a single matrix over the whole time period, depending on what you're trying to do here.
Can you clarify how you would like to concatenate the matrices and what type of export you have in mind? One way to do this would be to use the Standardize -> Concatenate signals process. You won't be able to manipulate the resulting object in Brainstorm since its dimensions will not be valid anymore, but you can export it to Matlab and all your connectivity matrices will have been concatenated in the first dimension of the TF field.
Let us know,
Martin