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Try this:

use strict;
use warnings;

local $/="\n\n";

while (<DATA>){
   if ( my ($prefix,$suffix)=m/\[WinEventLog:.+index = (\w+)_(pr|np)\s
+*$/s){
       # print "$prefix\_$suffix found .. replacing...\n";
       s/index = $prefix\_$suffix\s*$/index = window_$suffix\n\n/;
   }
   print ;
}

__DATA__
[WinEventLog://Application]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = CNDO_pr

[WinEventLog://Security]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = CGWS_pr

[WinEventLog://System]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = DMRW_pr

[WinEventLog://ForwardedEvents]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = NENP_pr

[WinEventLog://Setup]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = EOFK_pr

[WinEventLog://Application]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = FDWD_np

[WinEventLog://Security]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = ASKD_np

[WinEventLog://System]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = JMSF_np

[WinEventLog://ForwardedEvents]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = JCCD_np

[WinEventLog://Setup]
checkpointInterval = 5
current_only = 0
disabled =0
start_from = oldest
index = HSMS_np
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