Here's another way, featuring flock. It finds the first "unused" number when adding a new user, so the gaps are kept to a minimum.

#!/usr/bin/perl -- -*-fundamental-*-

use strict;
use Fcntl qw(:flock);

my $type  = shift or die "Need a type!\n";
my $title = shift or die "Need a title or user!\n";
my $desc  = shift || "";

my $flatfile = "members.txt";
## Format of file: ID|Title|Description

&AddUser if $type =~ /add/i;

&DeleteUser if $type =~ /delete/i;

die qq[Invalid type of "$type"!\n];
exit;

sub AddUser() {

  ## Add a new user to the flat file

  ## Open the file in read/write mode:
  open(FF, "+< $flatfile") or die "Could not open $flatfile: $!\n";

  ## Now we lock it so nobody else messes with it until we're done
  flock(FF, LOCK_EX) or die "Could not flock $flatfile: $!\n";

  ## Now, we read through until we find a "free" number

  my $goodnumber=0;
  my $newnumber;
  my $slurp="";

  while(<FF>) {
    $goodnumber++;
    ($newnumber) = split(/|/, $_, 2);

    if ($newnumber != $goodnumber) {

      ## We have just skipped a number - the perfect place
      ## to add a new user!

      ## Decrease goodnumber temporarily
      $goodnumber--;

      ## Save this spot, so we can go back to it quickly
      ## We need to subtract the line we just read in,
      ## because the new entry must go *before* it

      my $position = tell(FF) - length $_;

      ## Save the current line, since we have already read it:
      $slurp = $_;

      ## Now we slurp the rest of the file into memory:
      ## Setting $/ allows us to read the whole thing at once
      ## by setting the input record separator ($/) to
      ## nothing. See perlvar for more.

      { local $/; $slurp .= <FF>; }

      ## Now we rewind the file back to where we marked it:

      seek(FF,$position,0);

      ## This bails us out of the while loop
      last;

    }
  }

  ## Increment (needed in case no "holes" found before the end of the 
+file)
  $goodnumber++;

  ## Some systems need this to switch from read to write:
  seek(FF,0,1);

  ## Add the new entry:
  print FF "$goodnumber|$title|$desc\n";

  ## Add all the entries after that:
  print FF $slurp;

  ## We should not need to truncate, as the size is always
  ## increasing when adding a user, but just for fun:
  truncate(FF, tell(FF));

  ## Close and unlock
  close(FF);

  print "Added user $goodnumber to $flatfile.\n";

  exit;

} ## end of AddUser


sub DeleteUser() {

  ## Delete a user from the flat file

  ## What number user do we want?

  my $baduser = $title;

  ## Sanity check:
  $baduser =~ /^\d+$/ or die "User to delete must be a number!\n";

  ## Open the file in read/write mode:
  open(FF, "+< $flatfile") or die "Could not open $flatfile: $!\n";

  ## Now we lock it so nobody else messes with it until we're done
  flock(FF, LOCK_EX) or die "Could not flock $flatfile: $!\n";

  ## Now, we read through until we find the "bad" number

  my $newnumber;
  my $slurp="";

  while(<FF>) {
    ($newnumber) = split(/|/, $_, 2);

    if ($newnumber == $baduser) {

      ## Save the spot right before this user, so we can
      ## go back to it quickly later:

      my $position = tell(FF) - length $_;

      ## Now we slurp the rest of the file into memory:
      ## Setting $/ allows us to read the whole thing at once
      ## by setting the input record separator ($/) to
      ## nothing. See perlvar for more.

      { local $/; $slurp = <FF>; }

      ## Now we rewind the file back to where we marked it:

      seek(FF,$position,0);

      ## This bails us out of the while loop
      last;

    }
  }

  ## Some systems need this to switch from read to write:
  seek(FF,0,1);

  ## Add all the entries after the bad one:
  print FF $slurp;

  ## We do need to truncate, as the file size has shrunk:
  truncate(FF, tell(FF));

  ## Close and unlock
  close(FF);

  if ($slurp) {
    print "Deleted user $baduser from $flatfile.\n";
  }
  else {
    print "User $baduser not found in $flatfile.\n";
  }

  exit;

} ## end of DeleteUser
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