This is exactly applicable to the project I just started analysing this week! Argh! 
I should have known better than to start just before a new release.
My reads had been joined with fastq-join (still multiplexed), and then I imported them into Qiime 2 as EMP single-end fastq, then went through demultiplexing, quality filtering and deblur.
Could you please provide some more details about the difference between this approach and the new commands specific to joined reads described in this tutorial? Should I go back and re-import my data as joined reads instead?
Thanks!