Hi again! I just want to post the answer I got from WooThemes Support regarding this matter, as someone else might have the same issue, problems with large amounts of data not saving (variations, rates etc):
Hello Angela,
Thank you for contacting WooThemes! I’m happy to help you with this.
So this is a very common issue where your server is not able to handle that much data. It is not a WooCommerce issue. Please implement everything listed in this documentation to see if it can resolve your issue
http://docs.woothemes.com/document/problems-with-large-amounts-of-data-not-saving-variations-rates-etc/
Regards,
Roy – WooCommerceNinja
WooThemes Support