It seems that you are not really deleting lines from a file, more filtering the output of a command.

Would it be safe to assume that you would want to resume printing when the next line starts with 'array'? If so, I would suggest setting a print flag to 1 initially, and then in the loop setting it to 0 if 'unassigned' shows up, and reset it to 1 if 'array' shows up. Then print to output if the print flag = 1.

my %unitMap;
my $cmd  = "hpacucli ctrl slot=0 pd all show";;
open my $fd, "$cmd|" or return \%unitMap;
my $printit = 1;
while (my $row = <$fd>) {
        next if  $row =~ /^$|Smart/;
        $printit = 0 if $row =~ /^\s*unassigned$/;
        $printit = 1 if $row =~ /^\s*array .$/;
        next unless $printit;
        # moved processing to here; no need to manipulate lines you're
+ not going to print anyway
        $row =~ s/^\s+//;
        $row =~  s/[,|)|(]//g;
        print "$row";
}
close $fd;
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