Hello - is (was) the same for me.
- Flying over the area LOWL (Linz) + LOLW (Wels) > CTD
- LOWL = Airport of departure > CTD
- LOLW = Airport of departure > CTD
BTW: LOWL is my “home base” > BIG PROBLEM 
The solution in my case was:
- removing all content from the Community folder
- deleting the rolling cache
- deleting all *.dat files in the SceneryIndexes folder and
- deleting the Content.xml file
Next steps:
-
Start MSFS without content in the Community folder
A short flight from LOWL to LOLW (touch and go) and back to LOWL
Everything is normal/OK! -
Start MSFS with/incl. content in the Community folder
Everything is normal/OK!
BTW - look at:
This homepage > Home > FAQ > Promoted articles > How to restore the sim to its vanilla state (incl. file/folder location)
Liebe Grüße aus Oberösterreich