beet update on linked directory destroys database

I set up beets to link music on import.

```
import:
copy: no
write: no
link: yes
```

To inform beets about deleted items I tried to make an `beet update`. This triggered rereading of all metadata from the linked original files. Result: beets metadata mainly lost.

It is only a test setup, so I do not have a severe problem, but think this behaviour is unexpected and should be changed. At least a warning would be appropriate.

Reproduce the `beet update` path with the shown import and linked-directory configuration, then trace how linked originals are reread and metadata is written. Done means this case no longer silently destroys beets metadata or provides the requested warning, with regression coverage for the behavior.

Written by the indexing model from the issue text.