split removes the token it matched, but since you know what it is (here: $$$$ you can simply add it again.

Instead of slurping the whole file and then slipping, you can set the input record separator accordingly: 

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @records;
{
    local $/ = '$$$$' . "\n";
    while (my $record = <DATA>) {
        my ($stripped) = split /\nM END\n/, $record, 2;
        push @records, "$stripped\nM END\n$/";
    }
}
print Dumper \@records;

__DATA__
-OECHEM 658567-

1 2 0000 V2000
4 \t 5 8.7 7.655 3
2 \t 55 6 4 5
M END
> <compound id>
665765765
> <source>
db1

$$$$
-OECHEM 35343-

3 6 0000 V2000
1 \t 7 6 4.6 9
2 \t 45 0 3 5
M END
> <compound id>
3546789
> <source>
db1

$$$$

[download]

In reply to Re^3: Regex for matching and appending by moritz
in thread Regex for matching and appending by joec_

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.