Hey, as some of you might already know or even got into, the chunkloading items like the quarry, quarry plus and enderthermic pump are disappearing in some cases. We don't know for sure what is causing it. However, out of experience I know that there was an issue with the enderstorage mod (endertank and enderchest) in chunks which got loaded by another mod. So I assume that it might be something similar, I would suggest to try out tesseracts and keep us posted that we can track down the issue together. Edit: It is not related to the enderstorage mod. Edit2: We could track down the issue and solve it, your quarries should be save again.