That's what I thought. I actually did do the two 3DS thing but still you run out before a shiny even comes up. Just was more work than it felt like it was going to be. So that's why I've just been using MB as backup. The O-Power method would be great, but because RNG gonna be RNG, I don't have all day to work with O-Power to make it happen. I do remember my energy staying drained through SR. Which is what left me a bit confused and frustrated and bringing my second 3DS into it. Then at some point I just felt like it wasn't worth it. But good to know.
Well, if the power works when it's sent mid-battle (may need testing, you get notified if you're sent the power mid-battle though), then you wouldn't run out because you'd wait til you find a shiny then send the O-Power. Similarly, if it worked like it did for me, where the O-Power was refreshing every SR, it also becomes no added hassle, besides keeping the second 3DS running. But I dunno if that'll always work.
I did just test though and my O-Power energy didn't remain drained after an SR. Used Capture 3 which costs 6 energy, SR'd and came back with full energy.
Edit: So, I was gonna test how Capture Power works when sent mid-battle, but instead I ended up confirming the persistent O-Power from a second 3DS lol. Sent Capture Power mid battle, received it, caught a thing, SRd and now every time I SR, I receive a fresh Capture Power while in range of the second 3DS. As long as you get that working, that's probably a great way to go when SRing for people with multiple 3DS's.
Edit2: I continued my mid-battle Capture Power test. Without capture power, the odds were 50-60%, with capture power they were 100%. Attempted 10 times, sending the O-Power while in battle, and caught all 10. Very small sample size, but this is tedious to test lol. Have to SR the main 3DS to clear the o-power, close the secondary so it doesn't refresh the o-power, and SR the second 3DS to regenerate the energy every couple attempts x.x Since it's a small sample size I won't say it's confirmed, but it does look like it works when sent mid-battle.
Edit3: It's also worth noting that even with O-Powers, having a Master Ball as backup doesn't hurt. Level 3 Capture doubles your chances, but that still only brings you to like 13-15% on a sleeping catch rate 3 legendary with 1 HP. ~10% for paralyzed instead. Of course that's with a basic Pokeball/Luxury/Premier etc. If RNG really wants to screw you, it still can.