Official response, surprised how fast they got back to me–
Thank you for contacting Microsoft Flight Simulator Support today.
We are aware of an issue where, in some cases, flight plan from World Map doesn’t show correctly inside the cockpit and/or VFR map.
This is caused by Avionics and Aircrafts updates that started in January 2023. These updates improve the planes and make them closer to their real-life counterparts. The team responsible for these updates are investigating the issue.
We have seen this affecting the following planes:
Boeing 747
Boeing 787-10
Citation CJ4
All planes using Garmin Avionics (G430/G530, G1000, G3000, G5000)
We are unable to provide information when the issue will be fixed, but in the meantime, you can do the following:
Create your flight plan on the World Map
Write it down
Delete the flight plan
Choose only departure airport and gate
Select "Fly"
When in cockpit, enter the flight plan manually