There’s no wrong or right way to soft reset. Just save before you encounter and no matter how you power off the device, all is okay.
Think of it this way. When you don’t save your game and turn off the power, it deletes all the progress up to the point, technically. Everything that happens if you don’t save ceases to exist.
Basically, just save if front of the Pokémon you want to soft-reset, do what you need to, and reset. Repeat.
For the Regis in particular, you can knock them out instead of soft resetting and they’ll still be there. For the Swords of Justice, just save before the encounter, close the software, and reopen. Good luck!