Pry off the bookshelf crown molding and replace it with the one you like.

Remove the molding from the top of the bookcase and replace with the molding of your choice.

I have to ask: in the second photo, the one of the top of the door, is that a work-in-progress photo? If not, they need to come back and insert that last piece of crown molding.

Would you just go straight across the room then, so that the bookshelf wouldn't have it's own molding per se? The carpenter said he was going to stop it at that point and then continue outside of it. I'm not sure I understood him though.

You're right about that missing piece. Thanks for the reminder. I'll have it done this weekend.

Correct. The bookcase would not have its own molding at the top. In my mind, the problem with your carpenter's plan is that 1) the difference in appearance of the two moldings would look odd, and 2) there isn't a good way to start the crown molding on the right hand side of the bookcase because the bookcase molding flairs out. There is no good way to connect them.

If your carpenter is a good finish carpenter he would never have suggested working around existing molding. The missing piece over the door will require some detail cuts, so ask him if he's able to finish it out.

Like the others have said, the existing molding over the bookcase should be removed and any remaining gaps should be finished out.