use List::MoreUtils qw/ firstidx /;

for my $val ( generate() )
{
  my $i;
  #  Deal w/ "uninitialized variable" warning as appropriate.
  while ( -1 < ( $i = firstidx { $_ == $val } @array ) )
  {
    delete $array[ $i ];
  }
}

#  Later...

#  exists() here would go better with earlier delete(), but
#  then would need to generate list of indices.
my @save = grep { defined $_ } @array;