Just updated to the latest version 2.0.8 and had the same problem again:
Before updating I checked if woocommerce.css and woocommerce-base.less both had right chmod set, which was the case (even set them to 666 and the css folder to 777 to make sure that wasn't going to cause any problems). After the update the customized settings were gone and I had to copy the 'old' woocommerce.css and woocommerce-base.less files manually to the assets/css folder to make it work again.
It's not a very big problem, but it would be nicer if it worked automatically after every update, wouldn't it?
Isn't anyone else having this issue? I can't imagine..
Thanks for any reply in advance!