The current folder is meant to prevent these kinds of errors. Your main saves are never touched except at the moment it says it is synchronizing the folders when you are done, at which point it copies all the current stuff back into the main folder. If you shut off during that point, you'll corrupt your game. I'm not sure of the source of these latest corruptions, but in the newer versions, quitting out of the game during play using the OS should be fine.
So it sounds like we should clean out our "current" folder before re-starting DF if we didn't exit normally?
Could not cleaning it out cause issues? Or does DF get rid of anything in there when it is started?
The following thought experiment is pure speculation:
E.g., if you have a saved fort. You load it, try some stuff, and then kill the game using task manager. Presumably the current folder will still have data in it now. Then, you start DF back up and load the save.
1) Does having data in the current folder when the game starts mess things up? I assume it is expected to be empty when the game starts...
2) So, you load with a non-fresh current folder, and as you play, more things are written to it.
3) You eventually save and exit normally. The current folder is synchronized in, causing issues due to having old cruft in it from the time you killed the game abnormally.