To minimise flash wear, you could select the new animation only when the music partions get mounted read-only - IOW, once per sync. This would deal with the partial-write problem, as you shouldn't be pulling the power while syncing anyway.

Perhaps a timestamp would be useful for people like me who tend to sync several times when installing a bunch of new music (once after uploading with emptool and several times with jEmplode as I copy tracks into all the relevant playlists). Then, you could install the new logo only if the old one is more than a {day, week, etc} old.