Thought I’d feedback what happened in the end.
So I used the app to top up my wife’s Oyster card by £10 at 1008.
I can now see the journey history online which shows that two hours later at 1208 she boarded a 428 bus but the top up did not go on and took her to a -10p balance so an emergency fare was indeed charged.
Fortunately, the top up went on when I was there on the return journey at 1508.
So it seems that sometimes it can be more than two hours for a top up to go on. Lesson for me in the future is to top up the night before to make sure!!!