So something like this:

use warnings;
use strict;

my $scheduleData = <<SDATA;
SCHEDULE Unwanted
mu1
mu2
Nancy#mu3
 mu4
 mu2
END
SCHEDULE Wanted
mu1
mu2
Mindy#mu4
 mu4
 mu2
END
SDATA

my $agentData = <<ADATA;
Harry
Mindy
Nancy
Orlon
ADATA

my $defsData = <<DDATA;
Mindy#mu4
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "mu2"
Orlon#mu5
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "SOMETIMES HAS AGENTNAME Orlon"
Nancy#mu6
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "mu2"
Harry#mu7
 SCRIPTNAME "SOMETIMES HAS AGENTNAME Harry"
 DESCRIPTION "mu2"
DDATA

open my $schdIn, '<', \$scheduleData or die "Can't open 'Schedule': $!
+";
my %schedules;
my $scheduleName;

while (defined(my $line = <$schdIn>)) {
    if ($line =~ /SCHEDULE\s+(\S+)/) {
        $scheduleName = $1;
        next;
    }

    next if $line !~ /(\S+)#(\S+)/;
    ++$schedules{$1}{$scheduleName};
}

open my $agentsIn, '<', \$agentData or die "Can't open 'Agents': $!";

my $agentsList  = join '|', map {chomp; qr/\Q$_\E/} <$agentsIn>;
my $agentsMatch = qr|\b($agentsList)\b|;
my $wantedSchedule = 'Wanted';

open my $defsIn, '<', \$defsData or die "Can't open 'Definitions': $!"
+;

while (defined(my $defLine = <$defsIn>)) {
    chomp $defLine;

    next if $defLine !~ /$agentsMatch#/;

    my $lineout = $defLine;
    my $flag    = $schedules{$1}           ? 'Yes'    : 'No';
    my $wanted  = $schedules{$1}{$wantedSchedule};

    $wanted = $wanted ? " | $wantedSchedule" : '';
    print "$defLine | $flag$wanted\n";
}
[download]

Prints:

Mindy#mu4 | Yes | Wanted
Orlon#mu5 | No
Nancy#mu6 | Yes
Harry#mu7 | No
[download]

My eyes don't parse a wall of uppercase text so I changed strings to something I could work with. I also removed the irrelevant file opens and the code building %scheduleMatch from an external file. It is important to trim out needless code and errors to focus just on the task at hand (see I know what I mean. Why don't you?).

The key is to improve the parsing of the schedules data so that we have both the agent name and the schedule name together in the schedules hash. Then the test in the loop processing the defs data becomes trivial.

Update: remove duplicated lines at the start of the example code (bogus copy and paste :-( ).