Perhaps the following will assist you in crafting a complete solution:

use strict;
use warnings;

my %retrieve;
my $count = 0;

while (<DATA>) {
    next unless /^Retrieve_/;

    $count++;
    my ( $retrieve, $time ) = split;
    my ( $h, $m, $s ) = split ':', $time;
    $retrieve{$retrieve} += $h * 3600 + $m * 60 + $s;

}

for my $retrieve ( keys %retrieve ) {
    my $hms = secondsToHMS($retrieve{$retrieve} / ( $count / 3 ));
    print "$retrieve\t$hms\n" if defined $hms;
}

# For seconds < 86400, else undef returned
sub secondsToHMS {
    my $seconds = $_[0] // 0;
    return undef if $seconds >= 86400;

    my $h = int $seconds / 3600;
    my $m = int( $seconds - $h * 3600 ) / 60;
    my $s = $seconds % 60;

    return sprintf( '%02d:%02d:%02d', $h, $m, $s );
}

__DATA__
perform testing
Date: Nov-29-2012
Host: amg
Machtype: x86e_win64
mode: 7
ver: 1400
Build : A-01-10

-------------------------------------------------------------------
testcase Version x-20-17
-------------------------------------------------------------------
Retrieve_generic_assembly_(CP) 00:01:20
Retrieve_assembly_1_(CP) 00:01:32
Retrieve_assembly_2_(CP) 00:01:41
-------------------------------------------------------------------
xxx 00:47:03
yyy 00:47:31
************************************************** **
************************************************** **
-------------------------------------------------------------------
ggg Version P-20-17
-------------------------------------------------------------------
Retrieve_generic_assembly_(CP) 00:01:25
Retrieve_assembly_1_(CP) 00:01:35
Retrieve_assembly_2_(CP) 00:01:42
-------------------------------------------------------------------
xxx 00:47:03
yyy 00:47:31
************************************************** **
************************************************** **
-------------------------------------------------------------------
ggg Version P-20-17
-------------------------------------------------------------------
Retrieve_generic_assembly_(CP) 00:01:25
Retrieve_assembly_1_(CP) 00:01:35
Retrieve_assembly_2_(CP) 00:01:42
-------------------------------------------------------------------
pp 00:47:02
kk 00:47:36
************************************************** **
************************************************** **
[download]

Output:

Retrieve_assembly_1_(CP)    00:01:34
Retrieve_assembly_2_(CP)    00:01:41
Retrieve_generic_assembly_(CP)    00:01:23
[download]

The output shows the average time for each Retrieve_ in p10.txt.

The seconds are continually summed. When the data reading is done, the total seconds are averaged for each Retrieve_, and then printed in H:M:S format.

To process the two files, you could use a construct like this:

$retrieve{$retrieve}{fileName} += $h * 3600 + $m * 60 + $s;
[download]

The you could use the subroutine above to calculate both avg H:M:S--including their difference with a prepended minus sign, where appropriate. The last chellenge is to figure out how to print the Retrieve_ lines in your desired order.

Hope this helps!