Yeah this is the one single area of UE4 that can be troublesome- often folders that I had moved and fixed up and deleted, come back as empty folders on restart, and sometimes manually deleting or moving them within the project folder messes up the directory. It is very dependant on what you are moving, and seems to “sometimes” work correctly, as mentioned above. I’ve found the only method of keeping a clean directory is deciding on a hierarchy when starting a project, and stick to it, but sometimes if you have placeholder content, or you want to use some marketplace assets but not have them in the main directory, it’s a pain to try and correctly move them. Also I have found that batch importing textures only saved about 50% of the textures properly even after multiple saves, and on restart, the remaining textures were missing, so manually importing a few at a time and saving was the only method that reliably worked. The main problem seems to be using folders- I can usually move single assets around without a problem, but as soon as I’m moving a folder of assets (especially if that folder has more than a few assets inside or subfolders), things get slow, complicated, and rarely move cleanly. In comparison to everything else in UE4, where things just work without the user having to get too involved, this definitely seems like an area that could be simplified.