If you're hoping for some method of telling the filesystem to ignore, or return the first n bytes of the file to the freespace and so avoid copying the file, both the short and long answers are: no.

Then your problem becomes how to copy the file most efficiently. And perhaps the best answer is to copy it in place and so avoid forcing the filesystem to find another 500MB to fit the copy into.

Something like this (untested) code might fit the bill:

#! perl -slw
use strict;
use Fcntl qw[ SEEK_CUR SEEK_SET ];
use constant BUFSIZE => 64 * 1024;

our $RECLEN || die "you must specify the length of the header. -RECLEN
+=nnn";
@ARGV or die "No filename";

open FILE, '+<:raw', $ARGV[ 0 ]
    or die "$!: $ARGV[ 0 ]";

sysread FILE, my $header, $RECLEN or die "sysread: $!";

my( $nextWrite, $nextRead ) = 0;
while( sysread FILE, my $buffer, BUFSIZE ) {

     $nextRead = sysseek FILE, 0, SEEK_CUR
        or die "Seek query next read failed; $!";

     sysseek FILE, $nextWrite, SEEK_SET
        or die "Seek next write failed: $!";

     syswrite FILE, $buffer
        or die "Write failed: $!";;

     $nextWrite = sysseek FILE, 0, SEEK_CUR
        or die "Seek query next write failed $!";

     sysseek FILE, $nextRead, SEEK_SET
        or die "Seek next Read failed: $!";
}

truncate FILE, $nextWrite or die "truncate failed: $!";
close FILE or die "close failed: $!";
[download]

A casual test showed the program took < 4 seconds on a 500 MB file, though you can hear the disk thrashing as the system flushes it file cache to disk for several seconds afterwards.