Hi, i know the recommended method for upgrading NGUI is create a new scene, delete the NGUI folder and the re import it.
But if you're using any version control system, and NGUI is already in it (as in my case), it will break the internal folder structure, making the version system stop recognizing NGUI as a valid folder (Was on VCS, but now the control folders -such as .svn, .git, etc.- are gone and can't sync back)
I'm sure this is to workaround a unity limitation, but i feel a better way must exists.
Just my 2 cents.
Regards!