Further to this, it appears if you read the data back into the scanner and write it again, it wipes out the system choice (leaves you with a discovery setting with no system picked, same as before).
EDIT: Ignore the above - I forgot to read the scanner before I wrote to it the second time, so it blew away all the stuff I set in the scanner itself.
One thing I do notice is that you can't pick a system when creating/activating discovery, unless you are in range of it. (One system is listenable from my location but the radius in the DB is small enough that the system is shut off from here.) Temporarily turning off "Use Location Control" in the entry for that Favorites file gets around this.