Can Sync Apps, Calendars, Contacts But Not Music/Video

Hi all,
I have been syncing my iPhone 4 (iOS 4.2.1) very nicely with my iTunes 10 for a while now. New apps get reflected on iTunes, as do calendars and contacts. However, today, I tried to click 'Sync all Music' on iTunes and I am told that I have synced my iPhone to another library and then I had to erase and sync everything. I gather that that message means everything on my iPhone will be gone, which is obviously not something I want. Strangely, I have all my music in my iPhone.
I suspect this came about a few months ago when I tried to sync the iPhone with another computer. That worked to some extent, and then I switched back to my iMac. But by then I had updated the firmware to iOS 4.2.1 and started on a clean slate, so to speak. That probably explains why I have all my music on my iPhone. So it is very curious that I can sync my apps and not my music.
So my question is - are my apps being backed up nicely? If they are, I am willing to live with this situation until I get a fresh iPhone 5 and then sync everything afresh.
Appreciate any comments, thank you.

I believe you may see this warning if you had your iPhone set to manually manage music and you change it to sync. When you do, I don't believe it does much other than check to see if there have been any changes to the list of media to keep on the phone since the last sync.
I could be wrong... but I believe this is the case.

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Can Sync Apps, Calendars, Contacts But Not Music/Video

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