Salem

I ran my ore smelter before I logged out. When I logged in, it was empty. No iron, no dross, no fuel.

There was no break in. My settlement has a locked gate.

did you double check that you put ore / lime in it before you left?

had atown mate run the smelter without filling it once, put the coal in then got busy and lit it forgot bout the rest

Or put lime in but no ore, but this is the only other possibility. There's been a report of ore actually disappearing, but nothing can be confirmed and it's quite random so far if true.

I'd say no, the resources were present, I even checked my storage if something were left out. But seeing as how leaving something out can be a likely mistake, I have to be open to the possibility.