Hi @hennihi,
Thank you for posting! Indeed, even the "NEW-files" are not looking very good. Your "NEW" trimming parameters seem sensible, given the quality plots, so I do not think that parameter choice is necessarily the issue here.
What primers are you using? What is the total length of the expected amplicon? If you trim your dada2 reads too much, the forward and reverse may not overlap enough to join reads, leading to such a low number of output reads. If that is the case, you may need to just use the forward reads and discard the reverse reads, which are much lower quality (as often occurs).
You could also attempt to run dada2 just on the forward and just on reverse reads; if you get a higher output of reads, that could indicate that the issue is occurring during the read joining stage.
@benjjneb, do you have any other ideas what may be going wrong here?