Tags are always taken from the most recent valid signature on a user ID made with a certificate. When certifying user IDs the user shouldn't be able to overwrite their existing tags accidentally.
Copied from T6698#175165:
A solution I can think of that would be privacy respecting and user friendly would be to "If exportable is checked and any keys have text: Ask the user if the tags should be kept and then also include them in the new key sig, and otherwise remove them.Maybe with a don't ask again.
Since tags are kind of an advanced feature that I don't think is used by many but loved by some. So I think the vast majority of users won't see such a dialog.