I'm a pretty seasoned flier so still trying to figure out what happened. Here's scenario:

1. Booked a 3-segment trip: MSN>ATL>JAN (Mon), JAN>ATL>LGA (Thur) and LGA>MSN (Tue) so I could do my work thing in JAN and have a fun weekend with friends in Manhattan. Total fare = $933 in mostly K/L. I take MSN>ATL>JAN as planned.
2. After seeing forecast for NYC and change in some friends' plans, decide to utilize NYC change waiver and re-route JAN>ATL>LGA to LAX with corresponding return via MSP to ORD because that was $400 cheaper than MSN. The new fare is $1145 so an additional $212 which is fine since change fee waiver and work paid for most of trip.
3. I've now taken JAN>ATL>LAX. Feeling a bit ragged after we hit LA pretty hard for 3 days, including running a half, so want to go home early due to long work week ahead. I call PM line and request change fare quote for LAX>MSP>MSN 2 days early. She says I actually get a $460 credit AFTER the $200 change fee is applied. When factoring in saved hotel and rental cars (LAX and ORD>MSN), plus the trip I want, this is like a $1K swing in my favor. Of course I accept it and, in fact, the RUC is immediately successful for the last legs which are 10 hours later. I'm on the flight now.

When I look at the ticket email, it prices out the entire itinerary at $380. That's for MSN>ATL>JAN>ATL>LAX>MSP>MSN. When I had priced that out he Week before when I was deciding between LA or NYC this whole routing was ~$1400. Now it's $380? Is this a glitch? No way it ever priced out less than 4 figures especially with most changes last minute.

Of note, my miles earned on the flights taken are decreasing even after they've posted to reflect the fact that they have been repriced to really low levels. I am fine with this of course since MSN>ATL>JAN is never less than this whole itinerary priced out. How did I do it and how can I get it again?