It is not possible to delete the entire Favorite list at one time. You can only delete them one at a time, which, if you have a lot, no thanks.
But you can write over the entire Favorites list with another list. If this list happened to have, say, one item on it, well that would be pretty easy to delete.
We have the Favorites file 'Blank.prf' for this purpose. It resides at 3 Resources / AC / Favorites. It consists of a Favorite for the Hotspot tool, Archicad layer, pen 10, that's it.
On the flyout on the Favorites palette, choose 'Load Favorites', and open the Blank.prf file. You will get a dialog offering to merge or replace the current list. You want to replace. (Merge adds the new list to the old.)
Delete that hotspot fave and you've got your blank slate.
Why delete the Favorites? It helps clean out attributes. Attribute Manager will report that an attribute is in use if it is part of a Favorite. With no Favorites, it's one less place to look before you're sure you can delete something.
And of course you can clear them temporarily. Save the Favorites you are using, clear them, do whatever you need to do, then load your saved list back.