Here's another example based on hv's suggestion:

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"
[download]

This still has the problem noted by hv of mishandling ambiguous path-filenames. Given paths
    /unix/path/foo
    /unix/path/foob
how does one properly "correct" /unix/path/foobar.sh? The regex is designed to match the longest path (/unix/path/foob) in this case. See Building Regex Alternations Dynamically. (Of course, this problem goes away completely if one also knows all possible filenames that might be involved.)

Update: One approach to the ambiguous path-filename problem would be to capture all matches of the $rx_reference regex and report (warn or die) if there's more than one possibility. (If there's just one possibility, just fix it.) (This code has an interaction between regex (?{ CODE }) and a lexical variable, so it must use Perl version 5.18+. If your Perl is earlier, let me know and I can supply a simple fix. I'll just put the earlier version in as a comment. Also, use (?!) vice (*FAIL) pre-5.10.)

my @ambiguous;
BORKEN:
while (<$fh_b0rken>) {

    my @b0rken;   # can use with perl version 5.18+
  # local our @b0rken;  use re 'eval';  # pre-5.18 version
    $_ =~ m{
        \A (\s* CMD \s* = \s* " $rx_reference) ((?! /) [^\n]*) \n? \z
        (?{ push @b0rken, [ $1, $2 ] }) (*FAIL)  # (?!) pre-5.10
        }xms;

    if (@b0rken > 1) {  # more than 1 possible breakage: report ambigu
+ity
        chomp;
        push @ambiguous, join "\n",
             "'$_' ambiguous:", map "  '$_->[0]'?'$_->[1]'", @b0rken;
        }
    elsif (@b0rken == 1) {  # just 1 breakage: fix and output
        print "$b0rken[0]->[0]$add$b0rken[0]->[1]\n";
        }
    else {  # path looks ok: just output
        print;
        }

    }  # end while BORKEN

...

warn $_ for @ambiguous;  # report ambiguities
[download]

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