Beets import vs reimport and command line vs config.yaml

No. It says that it would move your files if you have copying enabled. But you have disabled it with -C (and also in your config).

The command line takes precedence.

It seems so, with your configuration. But if I were you, I’d make a backup just to be safe.

Nope—that’s exactly why we added the log file option, to cover this use case. The “normal” use case in this situation would be to move the files that get imported to another directory, so only the files that are left behind have been skipped. But if you don’t want that, the log file is the next best thing.