My understanding of this is that all the metadata of a thought is copied over when you copy to a new Brain database. If the thought has tags or thought types associated with it, it will carry those over. To not have the tags/types/events copy over to the new database you would have to remove them from the thought prior to linking, or copy the thought as text. (Update: Ooops, just saw Patrick said this exact thing, sorry to repeat).
If the thought being copied has a tag or type associated with it, and the database it is being pasted into already has that tag or type, you will have the option to overwrite or skip updating the tag/type information. If you overwrite, it will overwrite the existing tag or type with the new one. For example, database 1 has a tag that's green. In database 2 that same tag exists, and it's yellow. I copy the thought from database 1 into database 2 and choose overwrite. The tag in database 2 will then be green. If I skip, it will not overwrite the existing tag with the data on the new one. Continuing the example above, the tag will remain yellow in database 2. Hope this helps.