Ideally, the docker/VM related shares (appdata, domains, system) would have all their files on fast pool such as cache, and configured to stay there, with no files on the array, so Dockers/VMs will perform better, and so array disks can spin down since these files are always open.
Nothing can move open files, so you will have to disable Docker and VM Manager in Settings. And Mover won't replace files, so if anything exists in both places, you will have to decide which to keep.
Dynamix File Manager plugin can help you work with folders and files directly on the server.