Modern fobs (2007 and later Harley) are always "on", even when they are hanging on a hook in a closet or in a drawer, so those spare fobs either need to have their batteries removed when not being used or the batteries should be changed on a regular schedule. I've always recommended making that a yearly maintenance item. Also carrying a spare battery in the retail packaging somewhere on the bike is a good idea.
IMHO, the keyless systems currently being used in vehicles is a huge step backward in terms of actual security, and I try very hard to find vehicles that haven't had their security sacrificed to the "convenience" gods. It has become very difficult, as more and more manufacturers have joined the rush to jump on the bandwagon. I'm not sure that very many knowledgeable people have actually bought a particular model car/truck just because they didn't need to push a button to unlock their doors or they couldn't wave their foot under the bumper to open the liftgate, but the manufacturers have been pushing those sorts of "convenience" items since the beginning. It's really a cost reduction for the manufacturer, and that's the real reason they adopted keyless systems. Now crooks can hack your always on fobs and not only open your doors, but they can also just hit a start button and drive away just with that stolen code. No more two factor security, with an embedded chip in a physical key required to start the engine. I always find it funny that computer security experts push people to employ two factor security in the online world, but the vehicle folks do just the opposite.
Just my humble rantings,
Jerry