You may mean if one read is short, paired read won't be included either.
Would you help to find the parameter to change the minimum read to drop in phylosiftrc.txt?
If very short read retained passing the default removal, short read may be not still regarded as a hit generally for
"$align_fraction = 0.5; # at least this amount of min[length(query),length(marker)] must align to be considered a hit"
but paired read will remain if it has a hit, however if short read removed, paired read also will be removed: Is it correct and is it how the PhyloSift work?