Yes, that's a tricky compromise. Just in the case of the OP's wife's watch, it goes into a low battery warning mode, where it alternates one second advances of the second hand with a gap and 2 second advance. This probably drops the power consumption of the stepper a little but there's a limit to what you can do with just a second hand (the other hands being geared from it). I think more expensive models go into hibernation, where the on-chip counters continue to run, but the hand stepper is disabled until more power is received, at that point it re-syncs, clever stuff. With any solar (or battery) powered device, I guess you ultimately have to come to the conclusion that if somebody throws it into the corner of a dark drawer for 3 years, they no longer want it.
In the case of your product, based roughly on the thoughts above, I guess the questions you need to ask yourself are...
1. How critical is it's application? The more critical, the longer you want it to run before shutting down - effectively sacrificing battery life for performing its critical function for as long possible.
2. Can you provide any meaningful warning of low battery that can attract attention? That may allow you to delay shutdown for longer - assuming that the warning doesn't massively increase the current drain!). The watch and smoke alarm technique.
3. Can you implement any sort of hibernate mode as an interim step between operation and shutdown? - retaining timekeeping, volatile data etc. for instance.
4. How long, and how likely is it to get put away for a long time (presumably that makes it non critical)? If it's a long time then you obviously want to shut down earlier.
5. What battery chemistry (you're presumably talking Lithium)? Some are a little better at withstanding deeper discharge than others. Typically the ideal long term storage capacity is 40%. If you want absolute resistance against long periods of disuse this might be a guide, leaving a reasonable margin before battery minimum capacity is reached.
Without knowing something about the product, it's difficult to say more. You might want to start a thread on it in the Products and Design section (or Power and Renewable) as I suspect that this one is destined to sink into the mire of forgotten ones.