[Oleksandr Kramer]

Hello,

In the top part of the tree you see the system folders — so when you delete something there, the actual file is also removed from disk.

If your goal is only to hide or organize assets without touching the original files, please use Categories (the lower part of the tree) or apply filters instead.
That way the files remain in your system folder, and you just control how they are shown inside Project Manager.

Here’s a short video showing how filters work:

https://www.youtube.com/watch?v=HUQrljE_xFw

PS. You can hide the “delete file” menu item using Preferences