Hi @John! Thanks for getting in touch, sorry to hear things aren’t working for you.
The fix that @jairideout mentioned in the linked post specifically prevents duplicates from occurring in demux data on read or write. We took this strategy (compared to implementing some kind of one-off fix in denoise-paired) because the duplicate sample ids can be a problem in all kinds of other places, not just in dada2. Did you re-import your sequences using 2017.7? Or, did you use your previously imported sequences with 2017.7? If it was the second, the duplicate sample ids are still going to be a problem, and it would make sense to reimport them using the latest version of QIIME 2. If it was the first option above, we will get to the bottom of this! Thanks! 