Actually, you should have gotten 
s%
;\s+This\s+code\s+does\s+something\s+fancy\s+
enable\s+fancy_command\s+
wait\s+\(fancy\s+=\s+true\)\s+or\s+for\s+\$max_time\s+
if\s+\$\$error\s+=\s+\$time\s+out\s+
    write\s+"Oh\s+crap,\s+the\s+fancy\s+thing\s+didn't\s+work!"\s+
    deal\s+with\s+not\s+working\s+
else\s+
    do\s+fancy_command\s+
    write\s+"fancy\s+command\s+done!"\s+
endif\s+%TESTING
%six

[download]

which can be used as follows: 

perl -i~ -0777p sub.pl *.cstol

[download]

-0777 causes the whole file to loaded into $_.

Update: Oops, that command is the same as you gave. I've just tested it and it works. Perhaps you didn't have a newline after the last endif?

In reply to Re: Using Perl Regex to find & replace large chunks in code by ikegami
in thread Using Perl Regex to find & replace large chunks in code by jedikaiti

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.