I can't seem to find a way to update existing fields with new flags/flag settings that were added to the config after they were placed. I know removing and replacing them would work, but I don't want to have to force my users to do that every time I make a change to the config. Having some sort of command or automatic updating on reload would be amazing :)

It would be very useful, but at least in the latest version (Build 525/v10.0; I haven't tried it on any earlier version) I found while doing some testing that all fields placed in the world /should/ get the changed flags when the server restarts (Or the plugin is unload/loaded again in game by other means).

You can see this if you create an iron block field named "test v1", place it in the world, then use "/ps info" while in it to see the field type (Or give it the greeting flag) and stop your server. After that, change the field name in your config to "test v2" and start your server up again and repeat the "/ps info". The field should now be a "test v2" field with any flag changes you made included. It's a little beating around the bush and I'm not sure if this was even intended as the same thing doesn't happen then you use "/ps reload", but it seems to work.
I have not tested how this works on already placed fields with manually toggled flags or flags added with "/ps insert" in game so I don't know how they are influenced. I'm guessing they're not though considering I see no bug reports related to in-game field changes being lost.