Well, i am not VLuka
but i have some Flashpoint expirience
You are right! Update2, then 3 and finally 1.46 is the correct way of patching.
Now if you want to patch the game using your backup-cd then you will have to use the 'fixed' patches. If you want to use your original cd (higly recommended, because original=less things to go wrong) then simply download these patches and apply them.