In any command that uses oligo file to cull/bin/sort sequences there might be an option to keep all or some of those oligos. Maybe even an change to oligo files format - a tag noting if this oligo will be kept or not. (no tag will mean the default of not keeping - so all the previous oligo files will keep backward compability).
Right now only keepforward parameter comes to mind in trim.seqs command.
There might be several reasons to keep the oligos for some downrange processing, keeping the defaults as not removing anything will ensure that not problems are caused to those who have no need or care for such action.
pcr.seqs has a keepprimer option