Some of these issues are going to be solved by the “World Hub”, which sounds like it will work very similar to AFCAD.
[SDK Q&A Twitch Series: November 23, 2022]
Users will be able to fix up the airports themselves, and their changes will go back into the official build of MSFS. This is being released to alpha testing now.
If you haven’t, you should participate in this Bug Report and its vote for the saving issue.
https://forums.flightsimulator.com/t/flight-plan-lost-after-resuming-saved-flight/173081/149