Do you have a citation on the deliberately deleting non-iTunes Store music? I've used iTunes since version 3 and updated along the way. I've NEVER had a file deleted (and 95% of my music is non-iTunes Store)
Purely anecdotal, but it happened to me. I had ripped (using iTunes) about 200 CDs I own, over the course of a couple of months of throwing in a CD whenever I wasn't doing anything too important otherwise. These 200 CDs were joined by about 10GB of legally purchased MP3s from sources other than iTunes. In fact, I've only ever bought two albums on the iTunes store.
Anyway, some time after I had ripped and cataloged all of that old music, I decided it might be a good idea to back it all up to an external hard drive for safekeeping. I hadn't really paid much attention to file sizes or anything, but I knew I had about 36GB total. Curiously, after copying to the hard drive, I saw I only had about 25GB on there. This was too big a discrepancy even knowing I hadn't really looked at my library before copying. So I dug in, and I realized that the vast majority of MP3s purchased online were missing completely. There was an odd song here or there, but there wasn't a complete album (and I almost always buy the whole album in MP3 format) either on the backup or in iTunes itself. From what I could tell, all of my ripped music was there, but it was as if iTunes decided to "forget" that I also had all those purchased MP3s, and somehow had deleted them from my library without asking me.
Further investigation revealed that the few remaining MP3s were all available in the iTunes Store for purchase, and almost all the missing music was not available for purchase from Apple. It's mostly indie and obscure stuff so that in itself isn't surprising, but I found it intriguing that iTunes somehow deleted music that it couldn't have sold me. I honestly think that's more coincidence than anything, since a small percentage of the deleted music was available from Apple at the time, but it was frustrating nonetheless.
The story has a happy ending though: I had previously backed up my purchased MP3s onto DVD-R media, so I never actually lost anything. But that was the last day I ever used iTunes for anything.
Added songs to iTunes outside of the iTunes store, and months later went back to play the song but couldn't find it in iTunes.
The first few times I chucked it up to me being crazy and misremembering but by the third and fourth time I was sure I wasn't.
I started putting my iTunes directory in a git repo but that didn't highlight any files that got spontaneously deleted which made me wonder if they were really gone. I checked the filesystem and they were right there where they should be.
I'm glad to hear that it wasn't just me, for the longest time I though I messed something up because my friends who use the iTunes store almost exclusively had no such problem.
I'm still on the lookout for an acceptable iTunes replacement that is open source and that can talk to my newish iPod. (Smart playlists are a must)
I've used iTunes since OS 9 and have had a number of songs go missing over the years. This hasn't happened in a long time, but I always suspected that iTunes had somehow removed them due to mismanagement of the library. I didn't investigate further, but now I'm interested to hear how many others might have run into similar issues.
