It's not my library itself (the actual mp3 files) that changes, it is either a bug in itunes, or the .itl file that gets changed surreptitiously, though there isn't really any hint that has happened until I try to put something on my phone. At that point, I either have to lose it all and put it all back on (a time intensive process - syncing the iphone is not a speedy thing), or not put my new media on the phone.
I keep my mp3s backed up; I don't back up my .itl file; maybe I should back that up, though that won't guarantee avoiding the problem, as I have no idea when the libraries get out of sync (or whatever term is appropriate).
Again, as for playlists, I've never found them useful, unless they are ones I've built for a specific purpose. I'm very particular about my music, (and my digital devices) and want what I want, exactly as I want it. If manually managed music is less reliable, Apple has some work to do, not me.
I haven't ever found myself adding items to an empty library... it's more like the "serial number" (if you will) of the library has changed, and now itunes and the phone don't have the same serial number.