Theoretically, a full install of EB can be made over previous versions of EB.

However, in practice, we have had numerous problems internally with this. I have no idea why, because as you note, the versions should completely overwrite each other. It has been my practice to ask our internal testers to re-install EB from a fresh copy of RTW w/1.2 patch. I recommend this for all open beta testers as well.