I replace the CR123A annually. I buy them in bulk. I have 8 stations, 4 -1000 lumen flashlights (Light up the night, wait is that a squirrel in combat gear in that tree?)
To purchase them at the hardware store, drug store is too dang expensive. I use either Surefire or Titanium Innovations and they last. I pay about a dollar (US) for the Titanium Innovations and 2 bucks for Surefire . I get mine from :
https://www.batteryjunction.com .
Normally I wait until the console says the battery is low and needs to be replaced, but the weather is a big factor. If I have experienced a cold, cloudy winter, I will replace the battery in the spring, or if we have had an exceptionally intense bout of solar radiation I replace the ISS battery in the fall. Sure you can wait until you get "Low battery on station 1" and replace it then. but not to replace it, well when I do I can inspect the ISS case, check for corrosion.
As far as the Supercap. When I had mine bite the dust, I noticed that the corrosion was very near the cap bottom. I also noticed that the angle was tight, so when I replace mine, I used a wider bend, also put a bit of double sided tape, like they sell for mounting things to a wall. I read somewhere that putting that between the replacement cap and the circuit board would reduce shock by vibration. I have not idea why , it isn't as if the thing bounces around. But I did.
I did ask Davis about the second set of holes for a second supercap. Again not to use the 2nd . It was there by mistake. IF two are used, you don't get twice the storage but half. The charging circuit of the ISS isn't strong enough to gather enough energy to store, so it can muster about half and that would be the same as the one. As for it being a spare, nada.
I buy my super cap from Scaled Instruments and they are not that expensive. Do use a heat sink and a low watt soldering iron so not to fry the components.
OK... My two cents from my experience with the whole thing.