Hi Sam,
in dada2, it is recommend to use a value greater than or equal to 1 for the commoan "--p-min-fold-parent-over-abundance FLOAT". Thus can I ask the reason why you used a 0.75 for you data analysis?
I am not 100% understand the command, but please check this out: large percentage of merged reads flagged as chimeric, but not due to primers · Issue #602 · benjjneb/dada2 · GitHub
Ben @benjjneb mentioned that a higher value (e.g. 4/8) could prevent the FP chimera.
And also please check my post: The meaning of DADA2 command "--p-min-fold-parent-over-abundance FLOAT"
Recently I run into the similar issue, the sequence after merging is still good, bot after the chimera check, it lost ~80%. I tried to trim more sequences off and use the "--p-min-fold-parent-over-abundance 8" ~80% sequences are retained. I am now doing the taxonomy assign. I will keep updating.