Disappearing files
I created a subfolder, copied there some of the file from the folder at a higher level and deleted the file from there. Then I realized the copied files are gone from the new subfolder too. Does it happen automatically if I delete the same files from the folder of higher level or what is the problem?
If you want to remove an item from only one collection, right-click on the item and choose "Remove Item from Collection" in the context menu. Do not choose "Move Item to Trash".
Collections are explained here: https://www.zotero.org/support/collections_and_tags