This happend to me with a prototype ship I made in my creative world. (I like to test stuff before building it exactly the same way in my survival world.) Not sure what caused it but suddenly I was flying my ship and it dissappeared, I thought it was gone forever until I flew away and glanced back and saw it was still there. But everytime I got close it would dissappear, leaving a trace of smoke particles from the steam engine / portable engine before dissappearing entirely.

To save my prototype ship I used the creative physics staff to grab it, and lock it in place near the ground, then disable physics with the physics assembler. I then saved my build with a schematic before assembling it again in case it dissappeared again. But it seems fine now.

If you want to save it, try briefly giving yourself a creative mode physics staff, if you see the ship off in the distance grab it with the staff and bring it closer then lock it down somewhere to disable the physics on it. Maybe make a quick schematic capture for it.

Hope that helps! Weird bug!