I have had to make quite a few changes to your logic in order to get the desired result, but this works for the given input, and assumes that "the source file URL line is immediately followed by the line with the URL for its checksum file" is always the case. 
use strict;
use Data::Dumper;

my %HoH = ();
my $component;

while ( my $line = <DATA> ) {
    chomp $line;
    next unless $line =~ m/^\S+/; 
    if ( $line =~ m/^component=(.*)/ ) {
        $component = $1;
        next;
    }
    next unless $component;
    if ( $line =~ m/^version=(.*)/ ) {
        $HoH{$component}{"version"} = $1;
        next;
    }
    if ( $line =~ m/^sourcefile/ ) {
        my ($k, $key) = split(/=/,$line);
        # READ THE NEXT LINE
        $line = <DATA>;
        chomp $line;
        if ( $line =~ m/^sourcesum/ ) {
            my ($v, $value) = split(/=/,$line);
            $HoH{$component}{'sources'}{$key} = $value;
        }
    }
}    

for my $component ( keys %HoH ) {
    my $hash = $HoH{$component};
    my $version = $hash->{'version'} || '';
    my $sources = $hash->{'sources'} || {};
    print "$component: \n";
    print "version = $version\n";
    for my $key ( keys %{ $sources } ) {
         print "$key = $sources->{$key}\n";
    }
    print "\n";
}

print Dumper(\%HoH);

[download]

Output: 
HF: 
version = NULL
filename1 = checksum1
filename3 = checksum3
filename2 = checksum2

SVM: 
version = 10.0.70.102
filename4 = checksum4


'HF' => {
    'version' => 'NULL'
    'sources' => {
        'filename1' => 'checksum1',
        'filename3' => 'checksum3',
        'filename2' => 'checksum2'
    },
},
'SVM' => {
    'version' => '10.0.70.102'
    'sources' => {
        'filename4' => 'checksum4'
    },
}

[download]
Note: this method does not keep the order of the sources. If you need to keep the order then save them as an array of arrays like so: 
REPLACE
    $HoH{$component}{'sources'}{$key} = $value;

WITH
    push( @{ $HoH{$component}{'sources'} }, [$key,$value] );

THEN ACCESS
    for my $source ( @{ $sources } ) {
         print "$source->[0] = $source->[1]\n";
    }

[download]

In reply to Re: how to include an array of hashes in a hash of hashes? by tangent
in thread how to include an array of hashes in a hash of hashes? by anadem

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