I'm sorry, I misunderstood your question initially: I thought you wanted to compute a connectivity measure between signals of different duration. But obviously this is not the case.
If I understand well, you have multiple recordings of different duration, you put them all in the Process1 box and run the Coherence [1xN] process with the option "Save average connectivity matrix". But Brainstorm does not let you do this and you get an error message like this one:
What you are trying to do is correct for the estimation of Coherence, but the pre-loading of the files by bst_connectivity doesn't let you do it, as not all the connectivity metrics would work in this configuration.
As a workaround, yes you can compute the coherence values separately for each file and average them after. What you can do is to select the option "Save individual results" instead, followed by the Average process. To be tested, but I think it should give you the same results.