The Couatl engine is designed to automatically restart if there's a problem, in this case if Simconnect stops responding for more than a minute, which is completely abnormal, since we should be in constant communication with it, several times at a second.
However, even in that unlikely event, the automatic restart should kick in, so you can continue using the program even after such improbable event.
What is NOT normal, instead, the airport cache gets regenerated each time. This seems to indicate it always fails to complete, because in a normal situation, the airport cache should be regenerate ONLY if you install or remove a scenery, or the *first* time after an FSDT Live Update. Surely not during normal use or even a manual restart.
So you should provide a diagnostic log ( don't post it, but ZIP IT and Attach it to a post ), made after such restarts, which might hopefully indicate something about the failure to regenerate the airport cache, which is usually caused by corrupted scenery files.