Standard empeg software updates will destroy whatever is on the ``normal'' filesystems, from the standard software to anything else you might have added. However, new filesystems will be untouched. So the tradeoff is changing the empeg after software upgrades to mount the nonstandard filesystems or reuploading all of your programs (and their data) after software upgrades.

yes, but i was asking what the advantage of not using the drive0 and drive1 partitions in the first place. updates don't touch what's there. the only tradeoff that i can see is the negligible amount of music space lost.

EDIT: See my post below for my response to another small trade off. (Locking the music drives for syncs.)