I'm having the same issue with 4-digit track numbers being truncated. Like you, I've got lots of language lessons with track numbers well up into the 2000s - those numbers were attached to the downloaded podcasts (ChinesePod for you too?). Those numbers are important for filing. But unfortunately, whenever I change any other tag, the track number is reset - I guess only the first digit is kept, and the others are scrapped. iTunes then doesn't let you re-enter the original 4-digit track number. I believe it never has let you enter one directly, although it's accepted them if that's the way the track came.
Even undoing what you just did doesn't fix the damage - it undoes whatever other change you made most recently, but the track number change doesn't revert.
To repair the damage: Doug's Apple Scripts can work: "Put Track Prefix to Track Number" and, if I recall correctly, "Increment Number Tags" can also do it.
However, I wish the reset wouldn't happen in the first place. I've got most of these lessons with Media Kind = Audiobook (because iTunes has a bad habit of occasionally deleting old podcasts). And I've got them in playlists with repetition, but Apple broke those options for iOS devices when they moved all audiobook files to iBooks. So now I'd like to rename those language lessons as Media Kind = Music, but if I do that, I'll lose all the track numbers, which will really mess up the sorting. Doug's Apple Scripts can repair damage to a couple of tracks, but if you're repairing hundreds or thousands, it'll take forever.