How about adding a "Rename bookmark" button? Then, if I change the name
and hit "Save bookmark", I get a copy (which is what I also expect from
the UI).


Won't we have too much button here ?
If you think that the "Save button" shouldn't rename but save another one, I could change the behavior.
But imagine that you just want to update a search without changing the name (and without implementing the "Rename" button), then you should:
- load a search "MySearch"
- change the filters
- save the search with a new name "MyNewSearch"
- delete the old one "MySearch"
- load the new search "MyNewSearch"
- save the search with the old name "MySearch"
- delete the intermidiate search "MyNewSearch"

Could I suggest to add a confirmation alert when trying to rename a search ?
"Do you really want to rename the bookmarked search «MySearch» as «MyNewSearch»? To create a new one, please select «New bookmark»." (Please correct if needed.)

Another minor modifications could be to add a "as" between the select input and the text input.
"Saved bookmarked search: «New bookmark» as «SortByName»"
"Saved bookmarked search: «SortByName» as «SortByNameDesc»"

After your decision, I'll try to implement it. The choices:
- new button "Rename bookmark"
- new alert to warn the user (my favorite)
- add a minor text to be clearer

Hugues.