I usually use XML::XSH2, a wrapper around XML::LibXML, to process XML files. I tried the following: 
#!/usr/bin/perl
use warnings;
use strict;

use XML::XSH2;

package XML::XSH2::Map;
our ($path, $value, $v);

package main;

xsh << 'end.';
    open 1.xml ;
    register-namespace am http://www.abc.com/xml/appmanagement ;
end.

my ($replace, $add);
open my $PROP, '<', 'properties' or die $!;
while (<$PROP>) {
    chomp;
    s=^M_([RA])_/?== or next;
    my $action = $1;
    ($path, $value) = split / = /;

    xsh << '    end.';
        $v = //am:name[.=$path]/../am:value ;
        if $v set $v/text() $value ;
    end.
    next if $v;

    $path =~ s=/=/am:=g;
    xsh "set /am:$path '$value'";

}
xsh 'save :f new.xml';

[download]

This was the created file:

Removed per OP request (confidential data).

I am not sure that is what you exactly need, though. Especially in case of the last two lines of the properties file: the XPath matches 3 different nodes, it is not clear which one you want to modify.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: How to replace the existing values and to add the new nodes which are not existed based on the properties file by choroba
in thread How to replace the existing values and to add the new nodes which are not existed based on the properties file by perladdict

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