Repeatedly in my latest fort, I've had objects vanish, but still exist.
1. I had a marksdwarf shoot a couple goblins that were standing in a dry murky pool I'd drained. On death, there were multiple stuck-in bolts left in them. During a rainstorm, objects shifted. I could zoom to one of the bolts using the stocks screen, but the 'k' view of that tile had nothing. I unforbade the area, and that got them unforbidden, but still invisible. I unhid the area, to no effect. I made an ammo stockpile, and my dwarves went to the apparently empty square and picked up a bolt. They also picked up much more narrow junk than I expected, presumably also invisible.
2. Four goblins left their clothes littering my main underground hallway, so I poured magma through it. Some of the clothes burned, others vanished. But then, a year later, I had images seen and some of the magmaed clothes were picked up and decorated! The stocks screen revealed that there were still narrow clothes, some on fire, near but just downstream of where the goblins had fallen. No smoke though, and after forbidding, no more mystery narrow clothes appearing. But even several years on, the !!narrow crap!! is still there.
3. I have a number of molten obsidian I can zoom to. They have been on my list forever. It's hard to say for sure these were moved by the flow.
Item 3 sounds a lot like a known bug with a note that you needed a save before the event. I can't provide any saves for this report, sadly: no internets at home except on my phone.