I went to upgrade from Lion to ML, and halfway through installing it ran into a problem and said my hard drive was corrupted and I had to wipe it. I thought this would mean I couldn't update to FCE 4.0.1 since it would be a clean install and apparently that blocks the update.
When I was using Target Disk Mode (which somehow still worked) to load all my documents off before I wiped it, I thought I would try something. I went to an archived Apple Support document (http://support.apple.com/kb/TA38198?viewlocale=en_US&locale=en_US) for what to delete to uninstall FCE. Instead of deleting those files I copied them too. Once I clean installed ML I pasted the files back to where they came from, THEN reinstalled FCE from the disk, and everything worked in 4.0.1! All my old projects loaded, no featrues were broken, and everything on my mac is fine.
@ARTWW, I don't have Aperture, so I have no idea if what Apple's telling you is true or just them trying to sell FCPX. Unless Arpeture is some huge issue FCE did nothing to my mac, hopefully things work out at the Apple Store for you...but any Apple person I've talked to since Lion has always been pissy about me running FCE, and for me it's always worked fine, even on ML.