A couple other points to ponder:

print "Do you wish to update (Y/N)?\n";

You likely added the \n to ensure the prompt prints for the user. See $| to print without buffering, so you don't need the trailing newline:

$| = 1;
print "Do you wish to update (Y/N)? ";
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The overall structure leaves a bit to be desired. What about something more along these lines?

$| = 1;
my $choice;
do {
    print "Do you wish to update (Y/N)? ";
    $choice = lc <>; chomp $choice;
} until ($choice =~ /^[yn]$/i);

say "You picked `$choice'";
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This will repeat the prompt if the input is invalid, and normalizes the input by converting it to lowercase, to simplify your code later in the program.