if no one has anything similar to this already.

Nothing I've seen, so go for it.

My suggestion would be to use Math::Random::MT as the PRNG. It is portable and reproducible cross-platform.

Then something like:

use Math::Random::MT qw[ rand srand ];
use Digest::CRC qw[ crc64 ];

sub fingerPrintFile{
    my $file = shift;
    my $filesize = -s( $file );
    srand $filesize;

    open my $fh, "<', $file or die $!;

    ## assuming CRC-64
    my $chunks = int( $filesize / 8 ) - 1;

    ## Added sort per RichardK's suggestion below.
    my @posns = sort{ $a <=> $b } map 8*int( rand $chunks ), 1 .. 100;

    my $rawSample = join '', map{ seek $fh, $_, 0; read( $fh, my $chun
+k, 8 ); $chunk } @posns; 
    close $fh;
    return crc64( $rawSample );
}
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