@DBM, One of the other moderators reminded me of the following:
"dada2 does not throw away singleton reads. However, it does not infer amplicon sequence variants that are only supported by a single read".
I also forgot to mention that one potential way to retain more inferred per-sample ESV singletons is to apply --p-pooling-method pseudo --p-chimera-method pooled, as a read may exist as a singleton in a given sample but may appear multiple times across the entire dataset. These options should help. Again, others may have additional thoughts and can correct me, if I am wrong on this.