When the sketchbook folder is manipulated (i.e. a subfolder created, renamed, deleted, etc) from outside the IDE, the only way to have it updated is to restart the IDE (or maybe save some new trash sketch just to have the tree rebuilt).

There should be an option in some menu such as "rebuild sketchbook tree" or "refresh sketchbook tree" to update it manually without restarting the IDE.

Tag this as feature request if you like.