Translation:When did this accident happen?
From my understanding, the structure "是 (x) (y) 的 " basically translates to "It was (x) that (y)". In this sentence, the "是 (x) (y) 的" structure is "是 (在什么时候) (发生) 的". This translates to "It was (at when) that (happen)". Literally, the full sentence would be "This accident it was at when that happen?". Hopefully that explanation is helpful (and please anyone correct me if my understanding is wrong!)
I don't think so. 什么时候 already means "at what time" by itself, so no need to add 在 before.
I am not sure why 在 is there, but i assume it is used here to show that the action was in progress (same meaning as 正在). So a more literal translation of this sentence would be: "At what time was this accident happening?". But again, this is just a hypothesis. I hope someone will give us the answer.
在 is used before time words in other lessons to mean things like "on the weekend" (在周末) and on Fridays (在星期五). I still don't know why is is used here, but it seems to be entirely optional. Duolingo now excepts the answer without 在.
For 在 to show that an action is in progress, it needs to come right before the action verb.
"What time" has a narrower meaning than 什么时候. The answer to "what time?" is a clock time, such as "10:30" or "noon." You would only ask "what time?" if you already know the day, or if the day does not matter. The answer to 什么时候 might be a clock time, but it might be something else, such as "yesterday" or "a week ago." This is why "when" is a better translation for 什么时候.