I'm so glad you're having fun!!!
1 - I'm pushing updates as I have enough content to justify them! They'll be released as new downloads, but your save will automatically transfer over! So no worries about that. You can carry your team from here until the end of time, no work necessary. You can outright delete your game folder & be completely fine, your save is stored elsewhere.
If you're using the itch.io launcher, I don't know if that is true. I'm speaking about the standalone .rar download.
2 - I think you can reasonably expect updates to go one Gym at a time. Of course, we've got 16 Gyms here, so it might not be exactly what you expect... Gym 2 is on top of Mt. Moon, for example. So that'll be the scope of this upcoming update!