If you want to exclude certain blocks you need to keep track where you are in the file

use Modern::Perl;

# this is the list of sections to change
my @sections = qw/ messages secure cron maillog /;

# we put it in a hash for easy lookup
my %sections = map { $_ => 1 } @sections;

# Herein we remember where we are
my $section;

while ( my $line = <DATA> )
{
    # Remember the current section
    $section = $1 
        if ( $line =~ m| \[ monitor:// (?:  / ( [^/]+ ) )+ \] |x );
        
    # Change the index line if the current section
    # is one that interests us
    $line =~ s/ index = ([A-Z0-9]+) _ (np|pr) /**     index=LINUX_${2}
+/x #<-- you can remove the indent here once you see it works
        if defined $sections{ $section };
    
    
    print $line;
}

__DATA__
[monitor:///var/log/cron]
index=NDNW_np
sourcetype=syslog

[monitor:///var/log/maillog]
index=BSKX_np
sourcetype=syslog

[monitor:///var/log/secure]
index=NDNDK_np
sourcetype=syslog

[monitor:///var/log/spooler]
index=DNWN_np
sourcetype=syslog

[monitor:///var/log/audit/audit.log]
index=XBJB_np
sourcetype=syslog

[monitor:///var/log/messages]
index=JNJSJ_pr
sourcetype=syslog

[monitor:///var/log/cron]
index=NCJG_pr
sourcetype=syslog

[monitor:///var/log/maillog]
index=JE3K_pr
sourcetype=syslog

[monitor:///var/log/secure]
index=NLNDKN_pr
sourcetype=syslog

[monitor:///var/log/spooler]
index=EKJC_pr
sourcetype=syslog

[monitor:///var/log/audit/audit.log]
index=QKNK_pr
sourcetype=syslog
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