This will do the job:

my %newhash = map {
                    $_ => [
                        map {
                            { delete $_->{COMP} => $_ }
                        } @{$hash{$_}}
                    ]
                } keys %hash;
[download]

EDIT:

Or may be :

my %newhash = map {
                    $_ => [{
                        map {
                            delete $_->{COMP} => $_
                        } @{$hash{$_}}
                    }]
                } keys %hash;
[download]

depending on what you want as final result: your example is vague because you have only one element in the inner array reference

If it was my program I will be looking for result like:

{
    '103496-1' => {
        '1234' => {
            'FD' => '0010',
            'CLVD' => '5678',
            'Files' => [
                {   'hash' => 'a538346ad3485',
                    'File' => 'text.txt'
                },
                {   'hash' => '237d97892376a',
                    'File' => 'text2.txt'                  
                }
            ]
        }
    }
};
[download]

because you do not need an arrayref with just one element - hash reference. In which case use the following:

my %newhash = map {
                    $_ => {
                        map {
                            delete $_->{COMP} => $_
                        } @{$hash{$_}}
                    }
                } keys %hash;
[download]

Best regards