WP3 menus association lost when doing certain operations in WP control panel

Hello,

I am using WP3, and the WP menu mechanism. It works fine (much more flexibility!).

I noticed something strange however. I happened to delete all unused themes in my website (through WP control panel), just to remove unused items.
Then, when I loaded my website, the menu bar was messed up: it was using the Pages directly, not the WP menu.
I had to redefine, in the WP Menus panel, the association between the WP menu and the Atahualpa menu name, and it worked fine again.
No big deal, but certainly unexpected, since deleting unused themes should have no incidence on this. Presumably some other operations have such an incidence, but I don't know which ones.

Thanks.