I'm running emacs in daemon mode and usually have multiple instances of emacsclient open. Whenever I close down one of the client instances (with C-x C-c or save-buffers-kill-terminal) I am prompted to save all of the files currently open, not realizing that they'll remain open on other client. Is there a way to prevent this behavior?
What you observe is the correct documented behavior of save-buffers-kill-terminal.
What you need to use instead is C-x # (server-edit).