1.
itzak wrote: ↑05 Nov 2019, 12:40
placing a copy in the new location without removing the old video (.mp4, .mkv, etc) files.
Are you sure? This is highly unlikely. If FileBot performs a
Move / Rename operation, then it'll either work, or not work. If there's no error, then the move operation succeeded, meaning that the source file no longer exists. The operating system / file system typically guarantees this.

If you're using remote filesystems, then due to caching, you might see files that aren't actually there anymore.
2.
itzak wrote: ↑05 Nov 2019, 12:40
Because it's creating a new folder and not renaming, it is also leaving all the other .nfo, .jpg etc behind in the old folder.
Indeed, if you want to move a structure with arbitrary companion files, then you're out of luck.

Conceptually, FileBot can only work with Movie / Episode objects, and so matching a "series folder" to "Series" object would require a separate "Series" mode and that's thus not supported.

My approach would be the above, and then call the cleaner script to delete left behind clutter files, and call the artwork script to download missing artwork / nfos for the new folders. Some familiarity with the command-line would be helpful here.