Hi! Apparently, there are two likely reasons why your reads are getting filtered out. The first being from quality filtering, and the second from chimera removal. Did you check the stats to see if there were a lot of chimeras detected? If not, it's due to the quality filtering.
Having a lot of overlap will cause the merging to fail just like small reads that get over-truncated. Soilrotifer recommends in this discussion to adjust your truncation or adjust the parameter --p-min-fold-parent-over-abundance to 8 or 16.