Please read below posts talking about same issue:
No clouds or weather please read! Fix
Live weather stops injecting after a certain duration flown / certain time flown
Also see above post from T1ltN, he provided another workaround:
“So, I fixed my problem that I had live weather but no clouds since yesterdays Hotfix by not choosing custom weather and then go live weather but by picking live weather when launching the flight. IDK it is a weird bug I guess since before the update it worked the other way aswell.”