That last loop obviously is wrong. You cannot loop over a file handle. Certainly not over one that has been read to the end. Compare to below example and work out what you want exactly yourself

open my $fh1, "<", "final.csv" or die "final.csv: $!";
$csv->column_names ($csv->getline ($fh1)); # Read the header line
while (my $row = $csv->getline_hr ($fh1)) {
    $File1Map{$row->{username}} = $row->{date_modified}; # NO "my" the
+re!
    }

open my $fh2, "<", "HCDir.csv" or die "HCDir.csv: $!";
$csv->column_names ($csv->getline ($fh2)); # Read the header line
while (my $row = $csv->getline_hr ($fh2)){
    $File2Map{$row->{fullname}} = $row->{branch}; # NO "my" there!
    }
    
$csv->eol ("\n"); # Now use it for output
open my $fh3, ">", "completed.csv" or die "completed.csv: $!";
$csv->print ($fh3, [qw( user date_modified branch )]);
foreach my $user (sort keys %File1Map) {
    $csv->print ($fh3, [ $user, $File1Map{$user}, $File2Map{$user} || 
+"?" ]);
    }
close $fh3;
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