The Starbound website has details about issues that have popped up in the Early Access space game following the "Enraged Koala" patch, which has caused data loss. They've issued hotfixes to help mitigate this, and offer the following explanation:

WARNING: If you have not yet started playing, please make a backup of your ship file, which is located in your steam folder/player/*.shipworld and backups of your world files located in your steam folder/universe/*.world

CLARIFICATION: We’ve already pushed a partial fix for this issue that ought to prevent more containers from being erased. Please let us know if this is not the case.

A few hours ago, we pushed a second hotfix to Enraged Koala to fix an issue with seats and beds not being interactive. It worked fine in our limited test cases, but we quickly discovered after pushing from community feedback that it was deleting containers from some preexisting worlds. Some of these were things like the shiplocker and fuelhatch which cannot be legitimately obtained in the game, rendering that ship unplayable.

The only fix for this issue right now is to remove your shipworld and allow the game to regenerate them, or restore from backup if you have one. You will lose the contents of your ship if you do not have a backup.

We are all deeply sorry for the lost data, and will work hard in the future to prevent issues like this from occurring.

For those interested, here’s a quick technical write up on why this happened..