Win8 Strawberry 5.30.3.1 (64)  Tue 09/06/2022 17:27:14
C:\@Work\Perl\monks
>perl

use 5.010;  # need \K regex extension

use strict;
use warnings;

use autodie;

use Data::Dump qw(dd);  # for debug

my $file_paths = <<'EOFILEPATHS';  # known file paths
/unix/path/to/folder/is/here
/unix/path/to/folder/also
/unix/path/to/another/folder
EOFILEPATHS

open my $fh_reference_paths, '<', \$file_paths;

my ($rx_reference) =
    map  qr{ $_ }xms,
    join ' | ',
    map  quotemeta,
    reverse sort
    map  { chomp;  $_; }
    <$fh_reference_paths>
    ;
# dd '$rx_reference', $rx_reference;  # for debug

close $fh_reference_paths;

my $b0rken = <<'EOBORKEN';  # paths with appended files, some borked
CMD="/unix/path/to/folder/is/herefile_name.sh"
#CMD="/unix/path/to/folder/is/herefile_name.sh"
XYZ="/unix/path/to/folder/is/herefile_name.sh"
XYZ="/unix/path/to/folder/is/here/file_name.ok"
 CMD = "/unix/path/to/another/folder/some_file.ok"

CMD="/unix/path/to/folder/is/here/file_name.ok"
 CMD = "/unix/path/to/folder/alsosome_file.xy"
EOBORKEN

open my $fh_b0rken, '<', \$b0rken;

my $add = '//';  # make addition evident for development

BORKEN:
while (<$fh_b0rken>) {
    $_ =~ s{ \A \s* CMD \s* = \s* " $rx_reference (?! /) \K }{$add}xms;
    print $_;
    }

close $fh_b0rken;

^Z
CMD="/unix/path/to/folder/is/here//file_name.sh"
#CMD="/unix/path/to/folder/is/herefile_name.sh"
XYZ="/unix/path/to/folder/is/herefile_name.sh"
XYZ="/unix/path/to/folder/is/here/file_name.ok"
 CMD = "/unix/path/to/another/folder/some_file.ok"

CMD="/unix/path/to/folder/is/here/file_name.ok"
 CMD = "/unix/path/to/folder/also//some_file.xy"