As per Flixbus policy, you can take 2 bags with you:
hand luggage: this will go with you in the bus cabin. It can be 42 x 18 x 30 cm and can weight maximum 7 kg.
travel baggage: this will go in the trunk and it can be up to 20 kg. The dimensions allowed are 80 x 50 x 30 cm.
Luggage will be safe, but things happen in life. We heard some stories from people who saw luggage got stolen from the trunk!
There are even some impressive stories around South East Asia where they say some people hide in the trunk and take the valuable items from the luggage while the bus is driving.
I don't want to scare you here, but you should bear in mind that these things can – sometimes -  happen. Mainly, thieves are more active in big cities (such as Paris, Milan...).
Therefore, never, never, leave important belongings in the trunk. The valuable things (kindle, computer, money, documents...) must go on the bus with you.