End User Folders Disappeared - NOT in Trash

A few things to check (maybe you already did but worth a shot)

1. check to make sure this person was actually the “owner” of the folder(s) and it wasn’t just shared to them.  In the latter case, they wouldn’t see them in the trash, only the original owner would.
2. check to see if the folder(s) might have been accidentally moved into another location.  They can search for the folder name to see if became nested somewhere else
3. You can look at user activity in the admin reports (if you have access) to determine what occurred. 

@End User Folders Disappeared

“Since you’ve already checked the user’s folders and trash while logged in as them, the next place I’d look is the activity history and collaboration changes. In a lot of cases where content ‘vanishes,’ it turns out the folder was either moved to another parent folder by someone with edit rights or the user was removed from the collaboration, which makes the folder appear to disappear from their view.

If you have access as the admin, check the Reports → User Activity logs for ‘MOVE,’ ‘DELETE,’ or ‘UNSHARE’ events during the timeframe the user mentioned. Also confirm whether the missing folders were owned by the user or if they were collaborating on someone else’s content — that often determines where the trail leads.

If none of that shows anything, it may be worth opening a support ticket so Box can trace the item ID on the backend. Disappearing content almost always leaves an event trail, even if the user no longer sees it.”