... Can this damage the drive?

No, not really. unlink isn't some unpredictable magical fairy {grin}, however, user beware

#!/usr/bin/perl -T
unlink $ENV{HOME}
__END__
Insecure dependency in unlink while running with -T switch at - line 2
+.
[download]

It is possible that you're getting tainted data, and that combined with the forementioned documented behaviour ... i hightly doubt perl's unlink is the culprit.

Be sure to read perlsec (and turn taint on), and rule perl out as a culprit.

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