Just don't mix /mnt/user paths with /mnt/diskX or /mnt/<poolname> paths when manipulating files manually. Typically I only use /mnt/user paths to consume media or files, and disk paths to manage stuff in the background, but less technical users are encouraged NOT to directly access the disks, just use the user shares and the accompanying settings to allow Unraid to manage the initial and final file locations.
Much work has gone into removing the need to directly use disk paths for almost any scenario.
One of the ways I manually manipulate the system is to use the /mnt/user/domains stock location with cache : only settings, which means that when I use the wizard to create a VM, it's initially created on the assigned cache pool. However, I can manually move the VM subfolder for VM's I don't use very often from /mnt/cache/domains/NewVM to /mnt/disk1/domains/NewVM and everything still works without changing any VM path definitions. All my VM's show up in /mnt/user/domains, and I control which ones take up fast expensive SSD space, and which are relegated to slow cheap array space.
cache : yes and cache : prefer both tell the mover to do something, cache : no and cache : only tell the mover to ignore the share.