Honestly, I'm no help with this one. Looks like someone just finished reading Kondo's The Life-Changing Magic of Tidying Up. You start the process by taking everything out of storage places and put it on the floor! What's also interesting is what wasn't taken out. Let us know if it fixes itself.
i wonder if it has to do with the way they store items. some barns i think store by %. so say it is suppose to store "x" at 25%+ this and that to make up the 100%. if some how you made a diferent item all of a sudden that % would change. say you made ropes but hadn't before. the game math gets changed and it caused a glitch. instead of falat error and kicking you out of the game,it sent the workers to sort the barn instead. i'd be curious to see if they do put it all back. if they do save the game and compare hose items to what was in it before they did this. with the new limit flags there have been several hiccups with storage. i have had the log finder from the docks store all kinds of stuff including food and beeswax.
The bannies did eventually put it all back after I increased priority on the items. It happened to all the storage warehouses at the same time. I'm glad I didn't have to rebuild any because they were already upgraded from the storage barn. Strange, I will have to keep an eye on it.