In general, I usually create an upload to blank the keys 1st. - only the ones I'm changing - and then upload the changes. It just seems to work better with SDS errors for some reason.
But bear in mind, this may delete all members of a hunt group of keys, so you have to be cautious of that.
With speed dial keys you don't have to do this.
Also, you don't have to delete the labels. A button can be labeled without having anything assigned.
Ralph