i had a similar problem, items vanishing on deconstruction : after using cut&paste on a subfactory of many chemplants and assemblers (together with many inserters, belts, etc), only half of the subfactory was built and the other half stayed as ghosts because the machines seem to have disappeared :-(
since i use many mods (among them some that modify chemplants to be burner chemplants) i wasn't sure about what might have caused it and thus didn't report it yet. it also happened only very few times during all the time that i was using cut&paste a lot, and the advantages of these drones outweighed the small losses :-)
i have no idea whether a second effect might be related or a separate problem : in some specific cases, the drones are firing their red lasers to deconstruct something but nothing happens. thus they stay and try again a few seconds later, and again, and again, until i either deconstruct the building manually or until i use the deconstruction planner and unmark the buildings by using shift-drag.
since i have the grid enabled, i could see that every time that this happened, the machines to deconstruct were in one chunk (probably the same chunk that my char was in?) and the drones were standing on the first tile behind the border to the next chunk. no idea whether this observation is meaningful, but somehow it was strange :-)
this effect could be reproduced by cutting the same machine again, even several times, but sorry, i didn't think of keeping a save from that situation :-(