Hmm, it seems to me like it would be simpler to use a hash. In your loop, try: 
$hash{$refnum} = $scalar;
$refnum++;
next;

[download]
i believe that the problem that you are having now is because you are pushing a reference to an array onto an array. The expression $chunk$number (imagine square brackets there) doesn't really mean anything in the context of how you created @chunk, see?

well, i hope my ramblings helped somewhat, good luck.
-malloc

Update: Wow, these guys are fast. The two above posters explained things much more clearly, and we all got so caught up in the nonsensical array references that we missed your actual problem, which wog picked out nicely below, file clobbering. However, it should be okay to clobber the file in this case, since you are going to be rewriting the whole thing from your data structure, with the deleted entries removed, right?

In reply to Re: writing blank array to file? by malloc
in thread writing blank array to file? by dusk

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.