If you enter "Y", then $choice ne "N", so the OR clause is true and the while loop continues. You should have used && instead of ||.

Moreover, you can include the first reading of the input into the loop as well:

print "Do you wish to update (Y/N)?\n";
my $choice = q();
while ('y' ne lc $choice and 'n' ne lc $choice) {
    chomp($choice = <>);
}
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