Ive mentioned this before but dont know if i didnt explain very well or it cant be fixed.
I have the following flags in my config, and if i go outside and back into the area normally (walking jumping running) it work great.

  command-on-enter:
  - fly {owner}
  command-on-exit:
  - fly {owner}

However!
If i create a portal and go to the nether i can still fly in the nether, so i added

  ^prevent-portal-enter: true
  ^prevent-portal-create: true
  prevent-portal-destination: true

To stop players creating a portal inside the field with the fly command. But now if a player leaves the 'fly field and goes to the nether and then re-enters their area via a /home command the 'command-on-enter' doesnt fire.

I hope ive made this clear? lol
The problem this gives is that the fly command is now swapped ( the player can fly outside the field but not inside)

I hope

Just tested this like this.

  command-on-enter:
  - say "command enter"
  command-on-exit:
  - say "command exit"

When you enter into the nether "command exit" shows on chat, when you come back "command enter" shows. It works as it should. The problem here I believe is the fly plugin command which acts as a toggle. And when you change worlds it automatically disables flying. So when running the command again effectively toggles back on the flying.

You could ask the plugin author to add /fly on and /fly off commands so you can use them independently instead of a single toggle.

 command-on-enter:
  - fly on {owner}
  command-on-exit:
  - fly off {owner}