Diversity Analysis Across Samples, But Same Barcodes

We have three separate runs (Ion Torrent) that we would like to do diversity analysis on, but as I mentioned there are barcodes that have been used in multiple samples, i.e. Barcodes 1, 2, 3, and 4 were used in Runs A, B, and C. We cannot simply merge the .sff files and then do analysis because this would lump samples that are different into one barcode set.

What would be the best course of action?

Do the trim.flows, shhh.flows, trim.seqs steps for each run and then pool the output files. As long as your groups are named differently you can merge after this stage without consequence since the barcodes will be gone.