Hi @Arthy.
It is easy to learn. Every inspection check how much honey do you have and after putting hive back together lift hive by a corner just a bit. It helps to create a mental connection between amount of honey and weight. Empty hive is surprisingly light.
Do not worry about this. You always can feed sugar syrup to bees.
So do it! 
Nothing stops you from harvesting everything in the super, provided honey is ripe. Remove empty super from hive for the winter and feed them without any delay if brood box is short on honey.
If you don’t want to check and feed them often during the winter, there is one more option. Replace flow super with another box filled with waxed frames and feed them 2 parts sugar to 1 part water syrup. Prepare as much as your feeder holds, then another portion as soon as it is empty. Feed syrup equivalent to 8-10 kg of dry sugar in total. Don’t use queen excluder. We still have one or two warm weeks ahead of us, so bees will be able to build combs and fill it with syrup. Check hive weight around middle and the end of the winter to see how they go. Leave this box on next season and see how much do you like to run double brood box colony.
I know this advice is very different to those above. But the very first honey is not something to ignore 