In case the invoice contains goods that are originating not only from the EU but also from other countries (e.g.. China), and the total amount of the invoice exceeds 6000 euro, but the amount of goods originating from the EU is less than 6000 euro, is it possible to present the invoice as a proof of preferential origin of goods?

Yes, however in the invoice the EU originating goods should be clearly indicated, e.g. by marking the respective items, or by mentioning the origin of the goods in a special column for the purpose. Besides, the text of the invoice declaration should explicitly mention the preferential origin. In case the invoice contains goods of different preferential origin, all of them should be mentioned.