After changing a symbol, how do I update a device with the new symbol?
You can disconnect pins from the package one by one and then reconnect them. Press 'connect' on the device screen . Select connected device, then the pin/pad pair and press 'disconnect'. If you want to have a part in a package similar to one already present you can use 'copy from' dropdown on the same screen. 

Can't quite understand the issue though. On freshly created parts I shuffle pins around a lot till the  schematic looks pretty; they just stay connected to the package unless I attempt to change name in which case I'd have to disconnect first.