Music Player Not Displaying Songs?
I haven't looked exhaustively at the filesystem itself (didn't use adb shell or anything), but I'm fairly positive the warning is just a generic message that shows up whenever you clear data for an app or system service. I tried a couple of different apps and services and always saw the warning. After clearing my Media Storage data and unmounting/remounting my SD card I had:


All of my music still available (after it had a chance to rescan)
My Google Music account still set up and properly linked
My ringtone still set to the correct song on my SD card
All other accounts and settings normal


So basically, everything excepting the actual list of songs on my SD card was retained, and the list was refreshed after I remounted the SD card, as far as I can see.

Other than clearing Media Storage data, the only other thing I've tried to get my music to update is just unmounting and remounting the SD card (or using an app like SD Rescan to do it for you, as mentioned in the other question). I've personally had kind of mixed results with this, but the clear data then remount cycle always seems to work.