I had a setup similar to yours from this video https://youtu.be/hKJxlkeEZ8M?t=1138. I went to nether and left the machine drilling. When I returned the hole was already drilled but the machine was stopped at the second layer of bedrock with first layer replacing few drills. This resulted in the machine getting sticked to bedrock.

I made the same mistake second time. But this time instead of repleacing one drill, the whole platform disappeared and was replaced except the pulley (second picture).

What both of these accidents had in common, was that the machine was turned on when I went to nether, and when I returned it was already stuck.

TL;DR: Turn off your drills if you plan on visiting nether.

Picture of my setup

Still no fix over a year and a half later. This makes pulleys impossible to use and should be high-priority.

This issue has been marked as stale because it has been inactive for 3 weeks. It will be closed if it remains inactive for another 3 weeks.

This issue has been closed since it has been inactive for 3 weeks since it was marked as stale.

Same issue in v0.2.4. I am in singleplayer and I attached a creative motor to it on 256 speed, stood like ten blocks away for a few minutes and when I looked why it wouldnt come up again, I saw it had for some reason merged with the bedrock.

I had the exacly same problem. But we are in multiplayer.

First problem I had with disappearing parts was with a piston crop harvester machine, I put it in a faster clock connected to a gearshift, it zig-zag'ed a few times and the whole thing disappeared in front of me. Create 0.2.2b.

Then the second time was with this quary. When I turned the gearshift lever on, the whole driller (the chassis and the drills) disappeared. Create 0.2.2b.

Then we updated create to 0.2.3.
Our machine was running when we logged off, and this moring when I logged on, the "driller" and some other parts disappeared.

Kinda frustrating. Hope those are an easy fix :(