I had a similar experience, ALL folder Codex CLI (on VSCODE) touched were totally deleted in a very strange behavior. I lost tens of projects that I still didn’t have any backup for … some other folders just simply disappeared (for example, my downloads are in a “USER FOLDERS” folder on D:. it is still there and when I click downloads I find them. however, I cannot get into that folder and it doesn’t appear in explorer anymore, although I am showing hidden files and folders)
i noticed that while it was working on a folder named 00_DRAFTS ( I used it as a sandbox, it jumped up one level and DELETED all folders starting with 0 in its name , that is weird …. Another incident, I referenced another folder in the chat (outside my current folder), it deleted all its contents and put only one empty folder it was using ….