Yes -- you should be able to change both outbound and return at the same time during an online flight change by clicking the "Change this Flight" button in both directions prior to clicking the "Continue" button. (That's the sequence on the web, anyway; the app might be slightly different). If they're going to try to use multi-city search to get all of this onto a single ticket, they should be able to click "Add another flight" twice, but they'll have to ensure that the segments are in order, and frankly I'd expect the interface to error out at some point if you were to try this. It's just not that robust.

I took a quick look at the S fares -- and other related SFO-DEN fares, since you added that the fare buckets might have been wrong -- and I don't see any with a ¥20,000 cancelation fee (you mention ¥20,000 in another post). Most of the S fares are non-refundable; if they paid extra for a refundable fare, it looks like the cancelation fee is ¥30,000. However, each of the non-refundable fares that I see has a ¥20,000 change fee. That fee will be collected for any voluntary change, making this entire exercise moot if the cost savings is only $200; after paying the change fee, you're looking at a $65 net savings at current exchange rates.

Good advice.

Agreed. If the actual desire is to end up with two separate reservations -- presumably because the domestic fare is BE or because the discount fares aren't combinable end-on-end -- then it can't be performed in a single operation. OP's family member would need to change to NRT-SFO and then purchase SFO-DEN separately.