For Choice fare and above, just click “Change” and select the exact same flight. You will be refunded the points differential.

Under the “old” Southwest, there were no refunds for Early Bird Check In purchased if your preferred mode of operation was booking a new ticket then canceling the old one.

The Flight credit scenario OP you were concerned about would hardly ever happen. It only applies if you have bought a seat upgrade on a lower fare type, then subsequently upgrade to a higher fare type that includes the upgraded seat :

Extra Legroom seat are included with Choice Extra (previously Business Select)
Preferred seats are included with Choice Preferred (previously Anytime).

Anytime and Business have historically been a lot more expensive than WGA/WGA+.
The benefits (and reason to book those fares) was primary needing a fully refundable fare (or lack of WGA availability).
I can hardly imagine someone would decide to upfare to Choice Preferred/Extra after booking Choice and having paid for seat upgrade.