Disappearing boxes are well known and a big problem. Unresolved since early access. Here we discuss about this in a bigger topic:
I had just returned from my small voyage, and I discovered that everything I had in armorer’s bench, furnace and etc. disappeared. But content of my box inside a closed house with a bed was untouched (for now I have funrace and other working elements outside house, on foundations only).
So this is related to one of (all?) three things probably:
- decay system - things disappear like a bag of garbage you throw away from your backpack
- server restart
- your distance from your box/house - you are too far away and things disappear