Something like this: 

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

[download]
Output: 
DN: CN=Itmanagement,OU=Groups,O=uni.com
ChangeType: Modify
Add: uniquemember
uniquemember: uid=james,OU=Users,o=uni.com

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

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

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

[download]

If you tell me, I'll forget.
If you show me, I'll remember.
if you involve me, I'll understand.
--- Author unknown to me

In reply to Re: How to replace string in file2 that matches first column of file1 with second column of file1 by 2teez
in thread How to replace string in file2 that matches first column of file1 with second column of file1 by anakin30

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