Same thing is happening to me! I wanted to rebuild my vault because it was a mess! I moved the vault files to the cloud, but left the folder where it belongs. All other devices have sync closed. Right when I opened the vault all of the files that I moved into cloud are retiring! This has actually been happening if I deleted items off of devices, but I thought it was user error! I ended up with 13,000 files which is what prompted me to take the opportunity to start over! I thought I could fix this by moving the notes and now they are coming back! This has happened when I deleted files from my phone, my windows computer, my iPad and my MacBook. My vault is not in any type of cloud service.