I was having the same problems. Went on my favorite route...Southern California to Seattle, then to Anchorage, Alaska I did as a kid. Anyway I save it and when I load it the autopilot/GPS is all messed up, pause on the game is crazy, and I cant change the time (or weather) to reflect circumstances. Well I don't know if I can do anything about pause or time.
After hours of messing around I found the GPS had reverted to a previous waypoint and most of the settings such as altitude needed to be reconfigured. It took forever to learn how to select the correct waypoint something like flight plan, then direct to on the right side, but it eventually worked. It may have wiped out my IFR and I dont think I could start a new IFR.
So I'm frustrated I can't really save long flights, I think a better option is just flying as long as I can go, then using to the "fly to descent" option the next time I play. Hope they fix this. I love the game otherwise, it's a huge improvement!