I deleted the old SKSE files in the Skyrim folder and it still won't recognize the new one.
In my opinion, the SKSE people should be recommending that you save a re-named copy of the game executable, so that you can sometimes delay updating the game until they have re-engineered SKSE to deal with the update.
(Personally, though, I am not going to touch SKSE (nor alternatives like script dragon nor even autohotkey) until things get a lot more stable than they are now. At the very least, I am going to want SKSE to become "non-beta" -- I greatly admire the people that help out on the beta, but I just do not have enough time, myself, to deal with those issues.)