It only erases the TOP level menu stuff, IF you edited the xml file, outside of NEOedit. Yes there is a bug, where if you edit something you can potentially lose all your links to that device, but it is just that, a bug(I'm sure prontoedit, in it's infancy had plenty of bugs too).

With ver 1.3 it uploads ALL of what is in the NEO, including learned keys, so you won't lose anything when uploading then downloading.

I agree the inital software was horrible, but Philips is getting it right. If they fix the lose of links bug, allow editing of the top devices menu and allow direct entry of discrete codes, I will be a happy camper.