I think other posters have adequately covered the fact that emails of this form are SOP at T-24 when you have a waitlisted RPU/GPU that hasn't cleared for one or more segments.

The ambiguous part is "Why did they reference the LAX-SFO leg, when that's actually been upgraded already?"

My experience is that this isn't particularly meaningful -- it's basically a clumsy way of saying that some other leg isn't confirmed. I've got a few funny emails of this form, like the one where they tell me they can't confirm my upgrade from CDG-EWR, which is currently in R class. (I.e., the specific segment that they reference has already been upgraded).

If there's any meaning to it, it's probably that your reservation is out of sync. I usually find that when I have a reservation from AAA-BBB-CCC that's been thrown out of sync (usually by an upgrade clearing!) United's systems always refer to it as "your trip from AAA-BBB", because it can't make sense of the rest of the ticket.

But if you look at the res and don't have the red text saying to call reservations, it's probably just a meaningless screwup in the system. It almost certainly does not imply anything wrong with your LAX-SFO leg.

Nope. RPUs are used up if any segment clears. GPUs get returned if there was at least one international Polaris segment requested, but no Polaris segment cleared. Wacky emails have no impact on this behavior.