I've had this happen to one of my ships just this week. The ship was backed up as a work-in-progress previous to the galaxy update (new universe on the server), and I only just looked at it to bring it back into the game. On attempting to load it in I found the DATA folder and it's contents were missing.
The ship was saved to a new file name every time it was saved in the format 'shipname-yyyy-mm-dd' (Yamato-2014-11-07). The previous save (and all the others made) has the DATA folders intact and will load into the game no problems, but the most recent save will not because of the missing data. The file names have never been altered but are all what the game created as it saved.
This corrupted save of the ship also had a .sment entry in the exported folder. Attempting to import the .sment file results in the same missing DATA folder.
At the same time that I backed up this ship I also backed up the station it was docked to. The station will load in, but this ship is now undocked and spawn stuck in the other ships that are docked. Once you get the ship unstuck, then attempt to use it, the game will crash with a nullpointer when you press T to enter the weapons menu (trying to redock it with rails). Future saves of this ship will also result in a nullpointer when entering the weapons menu. Unbuilding the ship until it is just a core, then trying to enter the weapons menu still results in a nullpointer. I have sent a crash report in about this nullpointer using the report tool.
The Yamato-2014-11-07 ship is just a large empty partially built hull with no systems inside it. The previous save to the corrupted one is missing about 2 weeks worth of work on it (a lot of blocks).
This same thing has happened to a few players who have built their ships in single player, saved, then attempted to upload to the online server. They get me to check their blueprint when they get error message being thrown up about the missing DATA folder.
I have the .sment file of the ship missing the DATA file, and I can reproduce the nullpointer with the same ship that was part of the station save at anytime if logs of the crash are needed.