I've tested an tried this a lot if I am talking about what you're talking about.How do o-powers work with resetting the game? Do you get the entire time left when you saved back, or do you get no time back, or what happens?
Say I use an O power (capture for this example) on myself at 10:41 and save, then attempt to capture rayquaza which turns out to have not perfect ivs so I reset and load the game say 5 minutes later. I will not still have the O power as it seems from a technical point the O power is only active from 10:41-10:44 as those minutes would be in the 3 minutes of use for the O power. Also you still lose the O power meter point things that allow you to use them in the first place.
So you do lose the time and O power if you reload the game after the three minutes the O power was used for in the first place.