I was having the similar issue where the attributes would disappear after updating the cart. I tried to uncomment out the mentioned line in shopping_cart.php but still see that the attributes are disappearing. The actual name of the Text Field remains on my cart page it just strips whatever the customer input for that value. Does anyone else have this issue?
I double checked my shopping_cart.php file and this is the line I uncommented around line 81.
echo tep_draw_hidden_field('id[' . $products[$i]['id'] . '][' . $option . ']', $value);