use warnings;
use strict;
use Inline::Files;

my %name_change;

while (<FILE_1>) {
    chomp;
    next if /^$/;
    my ( $k, $v ) = split /,/, $_;
    $name_change{$k} = $v;
}

while (<FILE_2>) {
    chomp;
    s/(uid=)(.+?),/$1$name_change{$2},/ if /uid/;
    print $_, $/;
}

__FILE_1__
anakin,james
obiwan,nicol
skywalker,sarah
darthvader,robert

__FILE_2__
DN: CN=Itmanagement,OU=Groups,O=uni.com
ChangeType: Modify
Add: uniquemember
uniquemember: uid=anakin,OU=Users,o=uni.com

DN: CN=ComputerScience,OU=Groups,o=uni.com
ChangeType: Modify
Add: uniquemember
uniquemember: uid=obiwan,OU=Users,o=uni.com

DN: CN=accoutning,OU=Groups,o=uni.com
ChangeType: Modify
Add: uniquemember
uniquemember: uid=skywalker,OU=Users,o=uni.com

DN: CN=management,OU=Groups,o=uni.com
ChangeType: Modify
Add: uniquemember
uniquemember: uid=anakin,OU=Users,o=uni.com