They make standoff screws in different sizes so I'd think you could find a replacement. Typically from what I've dealt with, stand off screws have a slimmer male thread that screws into the motherboard tray and bottoms out against the hex barrel leaving a female thread hole. Then a hex cap screw is screwed through the mounting hole in the motherboard into the barrel of the standoff screw.
In the pic you posted of your setup, is that standoff secured to the motherboard tray or is it just resting there loose? Because it looks upside down (narrow part up and barrel against the tray) with nowhere to screw into. Maybe it's a different type of standoff, because in the second pic you posted of the standoffs I see some that look similar to...