As you know DADA2 will remove chimeras for you using a de novo approach.
Be sure to check the output of uchime-ref. There can be issues with the false-positive detection of chimeras when using usearch / vsearch with default settings. The reference sequence database being used and the parameter settings can affect how well uchime-ref can detect chimeras. There have been a few cases in which some of the most abundant OTUs were removed from the data even though they were clearly not chimeric based on follow-up checks.
To combat this, I've found that increasing the --p-minh to ~1.0 - 2.0 works well for 16S (decreases the sensitivity of detecting chimeras). But you should play with the parameters and sanity-check that the sequences flagged as being chimeric are reasonable.
One additional question: I have technical replicate for one of the samples - what’s the process to treat it during downstream analyses such comparing differential abundance.
As for your replicate sample, I'd consider the advice here.
-Best