If you decide to use iTunes, you can't go around messing with the files inside the library.
Just like you don't whip out your hex editor to fix PowerPoint presentations.
Make all changes using iTunes and everything will just work.
The only manual changes I made to my library were:
1) I manually dragged the folders that contained .wma files onto the iTunes application, so that it would import them; it converted them to .m4a files. Because for some reason, it didn't import them when I initially imported the library, despite them being in the same folder structure as all my other (.mp3) files. Once that was complete, each of those folders contained both .wma and .m4a files.
2) I deleted the .wma files from the library; I don't need two copies of each song on my local HDD.
After doing those two things, I didn't touch
my library from the file system. It was that way for nearly three months - all that importing was done in early July - and there was no problem. I added a few albums since that time, they went in just fine.
The other night, I noticed that a few albums were under the wrong artist; so I went into iTune
s and modified the artist name for those albums and clicked sync, expecting the result would be that iTunes would update the artist for those albums on my iPod. Instead, for some reason, what iTunes did was remove every last song that was originally .wma from my library and from my iPod. It physically deleted the .m4a files from my HDD.
There is no logical reason for iTunes to have interpreted me pressing the sync button as meaning delete half my library because the files were converted from another format; especially not three months after the fact.
I didn't delete those files; they're in both the backup I took in July, and in a backup I took very recently. There were several syncs between then and the other night, and none of those deleted anything. So why now?
So please, spare me the "it just works" bulls**t.