ive found that in every version of editor for me under no circumstances can an asset be renamed or moved if it is or has been open or a referenced BP has been open as this often results in duplicate or missing files or folders, editor crashes (with crash reports) and mostly editor not responding and having to force quit (no crash report).
Ive found only safe way to organise, copy, paste rename or even delete files and folders is to open project clean do not open any assets or BPs make changes to file structure as required then close and reopen project.