There isn't currently functionality for clearing, or re-ordering, entries in the favourite lists (although those things are logged as enhancement requests). You would instead just need to load each desired temperament ('Pitch | Load ...') individually and assign it to the desired slot.
johnstump_organist wrote:Mine is quite cluttered with double and triple entries for the same temperament, which I have no idea how happened
Note that if you load a cued favourite via a MIDI piston whilst the setter is turned on then the currently-loaded item will instead be assigned to the favourite slot.