20,000 lines is not likely to be more than 2M or so. That is not so big as to prevent slurping on most machines. The 40-some phrases in the junk file are insignificant in size, so lets compile them just once. 

use Fcntl ':flock';
my @regexen;
{
    open my $rx, '<', '/path/to/junk.txt'
      or die $!;
    @regexen = map {
        chomp;
        qr/\Q$_\E/
    } <$rx>;
    close $rx
      or die $!;
}

for (@list_of_files) {
    local $/;
    open my $fh, '+<', $_
      or warn $! and next;
    flock $fh, LOCK_EX;
    my $contents = <$fh>;
    # study $contents;  # may want to try this
    $contents =~ s/$_//g for @regexen;
    seek $fh, 0, 0;
    print $fh $contents
      or warn $! and next;
    close $fh
      or warn $! and next;
}

[download]
That should give decent performance. I've locked the file after opening to read and write, so you are protected from races.

Update: MidLifeXis' reply reminded me to chomp before compiling the regexen. Added to code, along with revised error handling in the big loop.

After Compline,
Zaxo

In reply to Re: file substitution by Zaxo
in thread file substitution by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.